I think that there are too issues here. Neither of which is the simple fact that she smokes. I don't smoke, and I don't like it when people smoke around me. If someone wants to smoke, and they do it where I can't breathe it, that's their choice.
The first issue is that she is obviously lying publicly about her "clean living". While the virgin thing isn't exactly confirmed, we do know that she drinks (I'm pretty sure there is evidence), and now smokes. These are entirely contrary to what she is telling people, and what she is saying she stands for. I don't see what the problem with the alcohol is. If they say there is a religious problem with it, they are lying. The Bible never forbids alcohol, just states that it should be used in moderation.
The other issue is that most of Britney's fans are 10 - 15 year olds, mostly girls. At that age, and since they are at that "do like every one else" age, people are afraid that this will encourage them to start smoking. It's sad that kids copy everything they see their idols do, but I guess it's part of human nature.