I don't think I can ever let my parents know I'm an atheist and with that seems to go my chance of having kids.
I know at first it sounds difficult because you care for your parents. But this is your life and whether they choose to respect your choices or not is up to them. If you want kids, have kids. If you want to be an atheist, be an atheist. If you want to dye your hair blue, dye your hair blue.
Your parents don't have to agree with your choices (as long as you're not breaking the law or anything like that)... but they should respect you and your choices.
TL;DR: Don't live for your parents, live for you.