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You've already gotten lots of responses, but I'll add mine. I've considered myself an agnostic since I was about 18. I'm married with two daughters; my wife is Christian. I've been able to discuss my agnosticism with my wife and she credits those discussions with her faith becoming her own instead of her parents -- she faced doubts that I raised, decided which parts she was okay with, and carried on.
We go to church each week. I go basically 1) to accompany her and 2) to keep track of what my kids are being taught. My wife and I have agreed that when our kids are old enough to ask questions, we'll make it clear that there are different beliefs (atheism is its own belief system), and the kids will be free to choose their own way. In the meantime, they are being taught the values espoused by Christians (who have no monopoly on them, of course).
I think that religion, whether true or false, has some value to some people. It helps them through certain crises and provides a stable part of their lives. Not enough for me, but to each his own.
So anyway, I guess my suggestion is: perhaps you can acknowledge the continuing importance of religion in the lives of your family members; they can respect that your beliefs no longer agree with theirs; your daughters can be allowed to make up their own minds. That will take understanding on all sides, and probably a few difficult conversations. If you show that you're not looking to change other people's minds, that may ease the blow for them. (Of course, you example may influence others without you trying.)