I don't have a lot of experience with kids. But seems to me that you're his father, you have as much say in his education as his mum does. If he is being lied to (even if his mother doesn't think that's what she's doing, religion=lying), be the one person who will tell him what's true and what's not.
And it's not really fair to him like you said. He asks you a question and he expects you to tell him the truth. It'll also help him understand for what is true and what is a belief. Something that seems to be nonexistent with the religious these days.
You may also want to consider that you want him to know you as who you really are. Rather than growing up and then finding out that this whole time, you were an atheist and didn't say a word to him. That feeling isn't pleasant.
And it's not really fair to him like you said. He asks you a question and he expects you to tell him the truth. It'll also help him understand for what is true and what is a belief. Something that seems to be nonexistent with the religious these days.
You may also want to consider that you want him to know you as who you really are. Rather than growing up and then finding out that this whole time, you were an atheist and didn't say a word to him. That feeling isn't pleasant.