I think you touched on both issues. The $6 after the fact (the fact being I already purchased my ticket) seems like such a petty way to make money. I've been on Continental on longer flights (Houston to Quito) and I've thought to myself "If they raised my ticket by $6, I would be fine, but asking for the money afterwards is so annoying." There's this mental block that I have, and I'm sure others, too, that after I've paid for my flight, that's it, no more charges or fees, I'm done.
As others have mentioned though, when it comes to searching for flights, we as consumers have brought this upon ourselves because more often than not, we don't distinguish based on features, we select based on price, so we have given airlines every incentive to pull these kinds of tricks. Once enough of "us" start buying the 4th, 5th or 6th most expensive fare because we like that airline's pillows/movies/flight attendants, then maybe things will change.