Well, personally I'm not in favour of infant baptism, but that's probably another debate. I would argue, though, that the choice hasn't been made - in most cases, the child is completely unaware of what's happened. They don't have any personal belief at that point.
I was raised by Christian parents. My younger sister and I were both taken to church regularly. I had a passing interest in religion, but no real belief. At 18, while I was at university, and after studying the subject for myself, I chose to become a Christian. My sister never did, and has no particular religious beliefs. So what does that mean? Was I indoctrinated and she wasn't? We both had the same upbringing.
I'd draw an analogy with a different kind of belief. I grew up in one of the safest Labour seats in the country. Pretty much everybody I knew voted Labour, or planned to when they were old enough. I clearly remember thinking, in my mid teens, that Labour was best and that a Tory government was about the worst thing that could happen to the nation. If you like, that was a kind of indoctrination. Nobody set out with the intention of indoctrinating me: that was the culture I was living in, and I absorbed it.
Eventually, I started to read about other options and I began to form my own political opinions, many of which moved away from the ones I was brought up with.
I think that's what should happen with religion (and secularism, come to that). All of us absorb beliefs from our culture, whether religious or not. Eventually, we need to test those beliefs for ourselves, and change them if we see fit. My parents and I are all Christians, but that doesn't mean we all hold the exact same set of beliefs on all points. I've changed my mind on some things, and I know they have too.
I don't say that's the way it always happens, but it is the way it should happen and, in this country at least, I think it's the way it happens more often than not.