Yeah, JL, I totally have that same feeling (re: circumcision), and think about it a lot.
Thoughts along the lines of "wait, why is it OK when we do it, but not them? Because... their gods seem really silly and obviously aren't real?"
I am lately going through a phase where I am struggling a lot with my feelings about religion. in terms of... kind of going back to arguably less-mature attitudes in re: "wait, people actually believe that an all-powerful being dictated this big book of rules and stories to us?"
I am totally into the idea that religion is this amazing force in human culture, which leads to both good and bad in society, brings people together, makes people happy, etc. I can accept this and respect this. There are a lot of things which have really moved me both in my life and in literature/media/whatever which have their roots in some really amazing ideas which come out of religion.
but sometimes I remember that it is all based on all-powerful creator of the universe. I have a hard time with that part.
And I really don't like the feeling that when I try to respect the beliefs of others, I am really just humoring them. Condescending.
And when I talk to some hardcore atheists i know, I come away feeling like this is what I am doing.