tzechuk, I think the reason that some doctors advise against flying in the first trimester is because that is when there is greatest risk of miscarriage. It is not that the flight itself is likely to cause miscarriage, just that if it does happen , it can be more traumatic for a woman who is away from home, in an unfamiliar hospital, new doctor etc. etc. There are some high risk pregnancies when they advise against flying at any stage.
And this is how controversies begin.
You see, from what I've read and been told, first trimester miscarriage isn't something that can be prevented - well yes, OK. If you get hit on the tummy or if you have a particularly traumatic experience, physically or emotionally, then sure, you can have a miscarriage that way. But most first tri. miscarriages occur naturally and I really don't believe that flying is going to cause you to lose your baby IF you are really meant to have him/her.
Except, of course, as you said - high risk pregnancies should avoid it. But they should avoid most things anyhow.