I'm really sorry i'm too tired to read all the replies but this was my situation;
DH is Catholic, I'm not anything. we got married in church as it was important for him.
We now have a DS and so DH obviously wanted him to be christened. I was honest and said that I wasn't completely comfortable with this as I think children should be allowed to make their own decision when they are old enough. DH sees being christened as helping DS to be brought up with a good moral and ethical foundation. Again it was very important to him, whereas I am not a "vehement athiest" so to speak. So I made it clear that as DS gets older I will explain my views to him re: God and religion so he hears both sides.
For the ceramony we told the priest that I and our chosen godmother were not Catholic or religious so would stand by the alter but would not say anything during the ceramony that we did not believe in (which was pretty much all of it!) We chose the godmother we did because she is one of our closest friends who will be a brilliant moral guardian to our DS as he grows up, and the fact that she is not catholic, nor christian, is by the by. The priest was fine with this (his Godfather is catholic).
At the party afterwards both my friend and I got some comments from friends and family about our silence during the service, but we explained our reasoning and that was that.
So I think the bottom line for us was - DH's faith is much more important to him than my lack of faith is to me, and DH has no issue with us bringing DS up hearing both sides and making his own decision as he gets older, but according to DH religious beliefs not being christianed could have reprecussions for him (assuming the catholics have got it right all along!).
And it REALLY annoys me when people assume we got him christianed so he can go to a good school!!!!