There's certainly going to be bias on both sides, but I do believe theist parents are more likely to "stack the cards" heavily in favor of their religion as opposed to atheist parents, who I feel are more likely to deal even hands to each religion and say something to the effect of "choose one or none; but do so based on the current evidence you have and not just because some authority figure tells you to."

The main reason for this has already been brought up I think, and it is the consequences of one's beliefs:

1. The theist parents love their child and are genuinely concerned for its well being (both future and present).

2. The theist parents firmly believe that all non-believers are not to be rewarded in the afterlife.

3. Moreover, the theist parents firmly believe that non-believers are to be most severely punished in the the afterlife.

I think it's logical to conclude that such parents are likely to raise their children to shun other religious beliefs to protect their child from suffering such a fate.

Atheists, on the other hand, typically do not believe in any form of afterlife; therefore making such threats of eternal damnation empty and non-motivational for believing in one thing or another.

The only reason I'm not with the fundies who seem to have Old Testament glued to their faces and shotguns glued to their hands is that Athiests have always struck me as reasonable, intelligent fellows who happen to not believe in God. So I'm sure they all will have freedom for their children until their community gets too big and we get Athiest fundies who bomb churches.

Religious families are more strict on their child's choice of religion because what kind of family that believes in hell would let their child be led astray from the beliefs of which they are so sure of.

I speak from experience on this debate, my mother took me to a church to expose me to religion but then let me decide if i wanted to keep going or not, thus i was free to choose if i wanted to believe in magic or reality - I chose reality

Probably. I'm sure there are plenty of atheists who immorally indoctrinate their children against religion. But I just think it's so much harder to do. How can you convince a child into believing a lack of something? Children are inquisitive, and would be reassured by a friend to watch over them. Telling them that there is no God is like telling them that Santa isn't real.

The time will come when they will form their own opinions. Leave children to their own devices, and you'd be amazed what they can do. The worst thing to do is to indoctrinate them. They are more willing to learn as a child than as any other age, and stifling that is wrong.

Unfortunately, the most popular theism threatens eternal damnation for choosing against them. So it is much more likely that if a child knows this, they will pick theism. There are no consequences for not picking atheism, so the child can make a free choice.