Steve Ray has a list of 35 loaded Questions for "Bible Christians" (quotation marks his)(link to the whole list). This is number 16/35. I'm trying to provide the answers in a common format, for easy reference.
16) If the meaning of the Bible is so clear—so easily interpreted—and if the Holy Spirit leads every Christian to interpret it for themselves, then why are there over 33,000 Protestant denominations, and millions of individual Protestants, all interpreting the Bible differently?
1) There are some things in Scripture that are hard to understand.
2) It is wrong to presume that everyone who reads the Scriptures are Spirit-led Christians - some are unlearned and unstable men.
3) We know that, because the Bible tells us so.
2 Peter 3:16 As also in all his epistles, speaking in them of these things; in which are some things hard to be understood, which they that are unlearned and unstable wrest, as they do also the other scriptures, unto their own destruction.
1) The 33,000 denominations claim is a lie that has been repeatedly exposed (example). Of course, Steve's lack of personal integrity isn't particularly germane to Rome's claims.
2) The church fathers agreed with us that things necessary for salvation are clear from Scripture. If the argument behind Steve's question is right, why do the church fathers disagree? Or, in other words, why was the obscurity of Scriptures only apparent in the post-Tridentine period?
3) Item (2) also highlights another point. Steve knows (or ought to know by now) that the Reformation principle of the perspicuity of Scripture is not that it is all perfectly clear, but that that the things necessary for salvation are sufficiently clear.