Probably because if you don't disable comments on religous blogs & video sites, atheists will dedicate their very existence to trying to argue, debate, bicker, and mock everything.
I mean, honestly, who wants to post a video and then have comments like:
"I hate you"
"there is no god so shut up"
"you're a f*** idiot. there's no god you moron."
It gets rather tiresome doesn't it?
Yeah, I run a blog, and I used to have comments. I can fully confirm that to get 1 respectful comment, you have to endure about 1,000 rude, abnoxious, defaming, and cursing comments. Do you want to sit around for hours all day sifting through comments and separating mature comments from immature insults? Just so that atheists can argue with you, which is nothing more than their opinion? Well, if you think you want to, then try it.
In fact, I can't even stand to read a religious article on AOL or CNN, because at the bottom it is nothing but a commenting war of people arguing and bickering.
I hate it.
Oh, and let me make this point. When an atheist or agnostic puts up a video about evolution, the dialogue is usually much different in the comments. Why? Consider this:
Atheists all agree with evolution, so they have no incentive to act ignorant, insult people, etc. But Christians typically avoid the immature/cursing comments when they post something. So it turns out to be a much more respectful tone.
But contrast that to a Christian posting something on creationism. Then what happens is that all of the atheists come and show their true colors, curse, and act rude. See the difference?
It isn't that we are afraid to defend or discuss our beliefs (or else we wouldn't be here!). Its just that it is annoying and frustrating to work on something and then you have to endure abuse and mockery.
EDIT: You aren't reading what I am saying. I am telling you the answer, but you don't want to hear. I am a Christian who has also turned off comments and that is why.
You say "respectful comments." If you allow ANY comments as a Christian, you will have to endure 1,000 rude ones to get 1 respectful one. Do you want to sit for hours each day moderating comments (thats how long it takes if you post lots of videos or blog posts)?