I have been Atheist since before my kids (aged 25 and 16) were born. They both know of my Atheism. Despite that, I have told them both they need to do their own research and make up their own minds on this topic. I've told them to NOT take anyone's word for it, not even mine. =] Hope this helps.

I told my (now ex) wife that we would let the kids go to Catholic School (they had a great education), Church on Sundays. But as soon as they were 13 or questioned why they had to go to Church I stopped holding back my opinions. In my case, I started with letting them know that I do not know if Lutheran or Catholic teaching are incorrect, I only know there are 1000's of different teachings about gods and dieties out there and that it was up to them to decide what they do or don't believe in. At last check, 1 is an proclaimed Athiest, 2 have no affiliation or want it with any church and 1 is a 3 day a year lutheran. I tell them all the time, that they are all right and no one can say for certain that any of them are wrong. Just make sure he is comfortable knowing you support what he believes is right for him as long as it does no harm to him or others.

Tell him the truth. It might sting for awhile, but your son will get over it eventually. Make it clear it's his decision to believe in fairy tales or reality. I wish I stopped believing in fairy tales early in life. Your son might be an happier when leaves the bs of religion/god. I know I am.

Be honest. Tell him you want him to make his own choices. Encourage him to learn more about his beliefs both inside and out of the bible in history and science. But let him know that you don't and that it was a personal decision. Share why if you wish but encourage him to keep learning and follow his heart and mind or find the balance between if they are in conflict about it.

"The God of the Old Testament is arguably the most unpleasant character in all fiction: jealous and proud of it; a petty, unjust, unforgiving control-freak; a vindictive, bloodthirsty ethnic cleanser; a misogynistic, homophobic, racist, infanticidal, genocidal, filicidal, pestilential, megalomaniacal, sadomasochistic, capriciously malevolent bully."
~Richard Dawkins

Be as honest with him as humanly possible. Don't hold anything back.

Try to explain your change of heart to your son in developmentally appropriate language. How old is he? You might also want to check in with him to see how he feels about the change. For instance: do you miss going to church? Do you miss praying? Did you like these things? If he did miss them or like them, consider finding substitutes. Maybe there is some other group you can go meet with regularly. As for prayer, ask him what he liked about it and see if there is some way to reproduce the experience without the spiritual component. On the other hand, he may say that he found it all tiresome and didn't like it anyway and good riddance!

It would be helpful if we knew how old your son is.

"I'm just not into that any more".to be diplomatic. Then share the truth as you know it and have all the answers (why?) ready. Of course you won't have them all, but make him understand love and caring does not stop without church and belief.

Honesty is always best in my opinion. He needs to learn, know and understand what is real and what is imaginary.

I agree, honesty is the best policy. Children are not Stupid, he will see religion for what it is?

Say to him what you just typed. We all have to make these decisions for ourselves. Best of luck!

Just say you're searching for answers and you don't think the church has them. There's nothing to be ashamed of or to hide from your son.