First, let me just say that I feel sorry for your parents. You've chosen to abandon a life of reason in favor of 5,000 year old Bronze Age superstitions written down in the middle of a fucking goat herd by barely literate primatives who thought that every animal in the world lived within walking distance of Noah's house (and that was a line ripped straight from Hitchens; yes I know who he is and he kicks ass)! So yeah, I pity your parents when you tell them. I don't pity you so much; you're the dumbass here.
But let's try to gain a little insight and perspective on your parents. What you see as intolerance is the result of a lifetime's worth of frustration at the ignorance surrounding them. I can relate to that! They're intolerant now, but I guarantee that they weren't always. There was probably a time when they were very friendly and understanding toward the religious people around them. And during that time, they got kicked in the gut by religious assholes more times than they care to remember. See, atheists would be perfectly happy to keep their opinions to themselves, except the religious won't let them! My own personal motto is "KEEP THE FAITH..... to yourself!" If you and Pat Robertson want to believe that Tinky Winky is gay and is therefore going to burn in Hell, well that's just fucking awesome for you guys, so why don't you sit there and believe it and leave everybody else alone?
That's all any atheist really wants. You guys just shut the fuck up, accept that not everybody feels the way that you do, and be happy with your own feelings of oneness with God and whatnot. You offer us the water of life, but we're not fucking thirsty, so you can have ours. Okay? Ok.
If only it were that easy. And that's why your parents are such intolerant dicks. They have long ago become fed up with trying to be tolerant and live in peace with the Christards. So, this is what you need to keep in mind when you "come out" to them. You need to stress to them that you're NOT one of those assholes. You need to tell them that you just want to believe what you believe and you don't care what anybody else believes and you're not out to "save" anybody or change anybody's mind, etc, etc.
It CAN actually work. In the time I've been married, I've gone from being a Christian to a Deist, to an agnostic, to an atheist, to a rabid anti-theist (the kind I used to hate). My wife is still just as Catholic as ever. How does that work out? Pretty fucking good, really, because I'm not trying to save her from her ignorant and backwards beliefs and she's not trying to save me from the fires of Hell. We both wish the other would change, but we accept that it isn't going to happen and there is peace in our home because we love each other enough to stay the fuck out of each others' religious affairs. As I write this, she's at church kneeling down and praying to an imaginary asshole who gave us sin, then made himself born as a human so that he could kill himself to save us from the sin he gave us in the first place. What a dick, and this is who my wife worships? This is who YOU look up to?
So be it. I think you'll find that your parents will be far more understanding and tolerant than you think they'll be. They will be hurt and disappointed that you've chosen to live in Never Never Land instead of reality, but they'll remember what it's like to be persecuted for one's beliefs (or lack thereof) and will not long do the same to you (if they do it at all). You'll need to give them a lot of reassurance, though. They'll be VERY worried about what you're going to become and you need to NOT be the asshole who tries to save them or anybody else. If you and your parents can do what my wife and I have done, things will be just fine. If not, then you guys are looking at years of war in the household until the day that you move out and even after that, there will be strain. They're intolerant because your "people" have made them that way, so you need to be the one to assure them that you're not like that and they DON'T have to be assholes about what YOU believe.
Hope I've helped. Really, I'd rather advise you to stop going to church and getting your brain washed and hung out to dry, but I know that isn't going to happen. You're finding yourself and your own identity in the world seperate from that of your parents. This is only natural, but I hope that in time you'll see the light of reason once again and come join us back here on the Dark Side.
All My Hate,