I thought it would be interesting to take a quick look at some of the extra apocryphal material Roman Catholics say Protestants wrongly excluded from the Bible. Remember, the common complaint is that Protestants don't have writings like Susanna in the Bible because Luther took it out. The doctrines taught in the apocrypha were said to contradict his teachings, so he removed them. Then, the rest of Protestantism followed him like sheep.
Luther's View
Of course, Luther did give his reason for not accepting Susanna and the other additions to Daniel: "We have uprooted such cornflowers (because they do not appear in the Hebrew versions of Daniel...)". But he translated it anyway and included it in his Bible saying, "And yet, to keep them from perishing, we have put them here in a kind of special little spice garden or flower bed since much that is good..." For Luther, Susanna "seem[ed] like beautiful religious fiction." If someone wanted to use it, Luther said "it can all be easily interpreted in terms of the state, the home, or the devout company of the faithful" [LW 35:353]. Luther being consistent with this either quotes or refers to Susanna in LW 11:112; 12:201; 18:330; 37:322; 44:223.
Jerome's View
That's outrageous isn't it? No not really. "The history of Susanna is certainly a Greek original, as was inferred by Julius Africanus and Porphyry from plays on words possible only in Greek" [source]. "Jerome places it at the end of Daniel, with a notice that it is not found in the Hebrew Bible" [source]. When it comes right down to it, Susanna is left out of the Bible because it appears to be a later addition to Daniel. It's questioned by Protestants on historical and textual grounds. It wasn't part of the Hebrew Bible. It's a later addition written in Greek, not Hebrew.
Roman Catholics were given a chance many years ago to come to terms with these facts. In responding to Porphyry's claims against the entire book of Daniel, Jerome grants he's made some good points in regard to the apocryphal additions:
But among other things we should recognize that Porphyry makes this objection to us concerning the Book of Daniel, that it is clearly a forgery not to be considered as belonging to the Hebrew Scriptures but an invention composed in Greek. This he deduces from the fact that in the story of Susanna, where Daniel is speaking to the elders, we find the expressions, "To split from the mastic tree" (apo tou skhinou skhisai) and to saw from the evergreen oak (kai apo tou prinou prisai), a wordplay appropriate to Greek rather than to Hebrew. But both Eusebius and Apollinarius have answered him after the same tenor, that the stories of Susanna and of Bel and the Dragon are not contained in the Hebrew, but rather they constitute a part of the prophecy of Habakkuk, the son of Jesus of the tribe of Levi. Just as we find in the title of that same story of Bel, according to the Septuagint, "There was a certain priest named Daniel, the son of Abda, an intimate of the King of Babylon." And yet Holy Scripture testifies that Daniel and the three Hebrew children were of the tribe of Judah. For this same reason when I was translating Daniel many years ago, I noted these visions with a critical symbol, showing that they were not included in the Hebrew. And in this connection I am surprised to be told that certain fault-finders complain that I have on my own initiative truncated the book. After all, both Origen, Eusebius and Apollinarius, and other outstanding churchmen and teachers of Greece acknowledge that, as I have said, these visions are not found amongst the Hebrews, and that therefore they are not obliged to answer to Porphyry for these portions which exhibit no authority as Holy Scripture...
But even Origen in his Vulgate edition (of the Greek Old Testament) placed asterisks around the work of Theodotion, indicating that the material added was missing (in the Septuagint), whereas on the other hand he prefixed obeli (i.e., diacritical marks) to some of the verses, distinguishing thereby whatever was additional material (not contained in the Hebrew). And since all the churches of Christ, whether belonging to the Greek-speaking territory or the Latin, the Syrian or the Egyptian, publicly read this edition with its asterisks and obeli, let the hostile-minded not begrudge my labor, because I wanted our (Latin-speaking) people to have what the Greek-speaking peoples habitually read publicly in the regions of Aquila and Symmachus. And if the Greeks do not for all their wealth of learning despise the scholarly work of Jews, why should poverty-stricken Latins look down upon a man who is a Christian? And if my product seems unsatisfactory, at least my good intentions should be recognized. [source].
Commenting on Daniel 13:54

'Tell me under which tree thou sawest them conversing with each other.' And he answered, 'Under the mastic tree.' And Daniel said to him, 'Well hast thou lied against thine own head; for behold, the angel of God, having received His sentence from Him, shall cleave thee in twain.' And a little while later the other elder said, 'Under the holm tree.' And Daniel said to him, 'Well hast thou lied against thine own head; but the angel of the Lord waiteth with a sword to sever thee in twain.'" Since the Hebrews reject the story of Susanna, asserting that it is not contained in the Book of Daniel, we ought to investigate carefully the names of the trees, the skhinos and the prinos, which the Latins interpret as "holm-oak" and "mastic-tree," and see whether they exist among the Hebrews and what their derivation is ---- for example, as "cleavage" [Latin (scissio) is derived from "mastic" [Greek skhinos], and "cutting" or "sawing" [Latin sectio, serratio] is derived from "holm tree" [Greek prinos, which resembles the Greek word for "to saw": prio] in the language of the Greeks. But if no such derivation can be found, then we too are of necessity forced to agree with the verdict of those who claim that this chapter [Greek pericope] was originally composed in Greek, because it contains Greek etymology not found in Hebrew. [That is, because Daniel twice makes a sinister wordplay based upon the Greek names of these two trees, and a similar pun could not be made out from the Hebrew names, if any, of these trees, the story itself could never have been composed in Hebrew.] But if anyone can show that the derivation of the ideas of cleaving and severing from the names of the two trees in question is valid in Hebrew, then we may accept this scripture also as canonical.
Commenting on chapter 14, Jerome says:
"And as soon as he had opened the door, the king looked upon the table and cried out with a great voice: 'Great art thou, O Bel, and there is no deceit with thee.'" The statement of Scripture in this passage, "He cried out with a great voice," may seem, because of its reference to an idolator ignorant of God, to refute the observation put forth a little previously, that the expression "great voice" is found only in connection with saints. This objection is easily solved by asserting that this particular story is not contained in the Hebrew of the Book of Daniel. If, however, anyone should be able to prove that it belongs in the canon, then we should be obliged to seek out some answer to this objection.
Dead Sea Scroll manuscript fragments have been found of the book of Daniel. To my knowledge, these fragments do not contain any of the Greek additions (the Prayer of Azariah, the Song of the Three Young Men, and the Story of Susanna). Jerome's appeal for proof has yet to be answered.
The Debate: Africanus versus Origen
"On the History of Susanna there is an interesting correspondence between Julius Africanus and Origen, in which the former denies the genuineness of the story and the latter defends it" [source]. You can read that debate here. Africanus notes similar textual problems expressed by Jerome above, as well as inconsistencies within the story itself. His letter is a quick read.
Origen's response is quite lengthy, but one argument in particular is worth noting:
But probably to this you will say, Why then is the “History” not in their Daniel, if, as you say, their wise men hand down by tradition such stories? The answer is, that they hid from the knowledge of the people as many of the passages which contained any scandal against the elders, rulers, and judges, as they could, some of which have been preserved in uncanonical writings (Apocrypha).
Origen goes on to describe those Jews that hid the books as "the rulers of Sodom." Schaff states, "Origen tried at great length to refute these objections, and one of his arguments is that it would be degrading to Christians to go begging to the Jews for the unadulterated Scriptures" [source].
Roman Catholic apologist Gary Michuta questions "just how many third century Christians Africanus may reasonably be supposed to represent" and that his opinion was based on his own "private study". Couldn't the same be easily said about Origen's view as well? Michuta says Origen's opinion is based on "an appeal to near-universal acceptance in all the churches of God" [Why Catholic Bibles Are Bigger, pp. 91-92]. Simply because the church read Susanna, doesn't make it canonical.
Michuta appears to embrace Origen's argument that "it is an offense against God to consider that the Jews, who rejected Christ, could somehow have preserved the true collection in pristine purity over and against the Spirit-filled Church" [Ibid. p.90]. A response to both Origen and Michuta was given by Paul in Romans 3: Then what advantage has the Jew? Or what is the benefit of circumcision? Great in every respect. First of all, that they were entrusted with the oracles of God.
Conclusion
"whatever may be thought concerning these literary or historical questions [about the extra-chapters of Daniel], there cannot be the least doubt that in decreeing the sacred and canonical character of these fragments the Council of Trent proclaimed the ancient and morally unanimous belief of the Church of God" [The Catholic Encyclopedia].
That really is the bottom line- when it comes right down to it, the reason Susanna is part of Daniel in a Roman Catholic Bible is because Trent infallibly said so. The Protestant takes Romans 3 quite seriously. The Jews were entrusted with the oracles of God. Their Bible does not have Susanna. Linguistic problems show the book was not of Hebrew origin, but Greek. It was a later addition to the text, rejected by the Jews.