I don't know why I have always had to take my kids out of carriers! I always hear stories of other people being allowed to leave them in, but TSA always acts like I am crazy when I ask to do so. And this is in multiple different airports and with at least three different types of carriers. Ugh. So annoying! It has been a year or so since I have traveled with a kid in a carrier, so maybe I will have better luck next time.
I think they've become a lot better about carriers recently. DD and I have been averaging 8 flights a month since August, and I have yet to be asked to take her out of the ergo. But when DS was younger I carried him in the ergo from 2008-2010 and was always asked to take him out.
They didn't have the scanners when I was pregnant w/ DD, but with this pregnancy (I'm 25 weeks) I've always travelled with DD and they don't make us use the scanners because it's their policy not to separate you from your child. If I weren't traveling with her, I'd opt out of the scanners even though they say it's about as much radiation as your cell phone.
The last time we flew at an airport with the scanners, it was so disorganized and we were there at 6am and they had ONE line open, despite several flights checking in. It was like the TSA agents didn't know how to use the scanners yet.
So when we fly in a few weeks I'm opting out. I would probably do the pat down anyways since I can't stand disorganization or the TSA.