Well the obvious bit is that they protect the priests because it's a PR problem. It's like when you notice the police never seem to turn one of their members over to the wolves for abusing their own position. It's worth saying that most of these problems are because it's an institution that exists first to preserve itself, if it wasn't it wouldn't be around at all.
And "Christianity Preaches Blank" is rather like "Science Tells Us Blank." It's just a setup to an ugly strawman version of religion. The Chris Hitchens style bombast is entertaining and not bad when it comes to dispelling plenty of bad assumptions people have about their religion, their institutions or their history. But bad science doesn't discredit science anymore than a bad dentist discredits dentistry as a medical field.
You need the best form of the other side if you want to argue with it, otherwise what you're really after is dogmatism or institutional solidarity or political smokescreens made to distract voters from practical reality. Not that those things aren't bad but it's not like the a christian philosophy is the root of it. It would be much more important if you were a christian having to argue with your own tribe, which I think is where the changes come from.
That's more a practical point but at the very least it's more interesting to argue with the better opponent.
Which you'd think a bunch of priests, men who'd dedicated themselves to their faith, would be a little more eager to get rid of, rather than harbour, proven pedophiles in the church if what they believed in was doing what's right and better mankind, yes?
What the Vatican has done to children does little to colour my opinion on Christianity; it's a horrid thing, but I don't recall a point in the Bible where it said 'And he shall rape little boys in lieu of women'. I can't fault Christianity for something which some of it's followers have done, unless the Bible or it's teachings are directly responsible (However, there is a lot of evidence pointing to the fact that Catholicism not allowing priests to marry or have sex, if I recall rightly, is in part responsible for attracting those to the faith who may lean towards doing those kind of things. But I have no opinion on that).
They are two seperate things; science is the easy one to point out in this case. One scientist can tell me gravity doesn't exist. One scientist can tell me it does and point to peer reviewed study which shows gravity exists. Even further, I can test this myself; if I drop something, it will hit the ground, just as the research states. Of course, with religion, you do have to paint with a slightly broader brush; stating what each subset of Christianity believes and which they prioritize over others would take forever, just for the major sects, let alone every minor offshoot of each of those sects and even then, the people within those sects can still hold other things more important than what their own sect/church preaches, so really, the only way I can discuss a topic like 'What does this religion preach?' is to focus on one focal point.
I don't know many Christians who refuse that the Bible is the word of God, and contains his teachings on morality and life, so I will state right now that my observations of Christian morality come from what is stated in the Bible, the same Bible I myself believed in during my younger years. Heck, even then, I have some problems (One guy says being a Christian gets you into Heaven, but Jesus then says that good deeds make you a Christian, not being a Christian, so even the Bible doesn't know whether it's coming or going).
As you've said, bad scientists or bad dentists don't discredit their fields; I completely agree with you. By the same extention, just because someone of a certain faith does something, good or bad, this does not reflect the values or validity of how good a religion is. You get into very weird loops that by doing something one group considers good, you're actively making yourself a bad example within your religion. Going by religion, helping your friend out by covering his shift on Sunday makes you a bad Christian who deserves to be stoned, despite the fact that your friends and most other people would say 'Yeah, he's a pretty nice guy'.
I mean, sure, I can get the best from both side. Depending on what you mean by 'best'. Do you mean the Christian who helps people, runs a soup kitchen and a shelter and cares for the rights of homosexuals? Or do you mean the Christian who actively is a 'good Christian' in the sense that he follows the teachings of his belief the closest, the man who stones women for being found to not be virgins, the man who stones his children for speaking back and the man who makes his raped daught marry her attacker in exchange for money? In other cases, this simply doesn't work. How do I argue what the 'best Atheist' is? The best Atheist does what every other Atheist does; doesn't believe there is a supernatural being who controls the world, because that is all Atheism states. It'd be like trying to argue what the best homosexual is; I mean, if you're a homosexual man who goes around having sex with women and not men, then you're doing pretty poorly at being a homosexual, for example...