I already mentioned this higher up, but so I'll try to summarize how it works (I was off put by how they were charging, too)
Amazon only charges for data and services that move through Whispernet over 3G. Amazon makes it super easy to control your spending if you decide to use 3G Whispernet services in your account, too. You can set limits on a maximum individual charge, which prevents you from accidentally sending enormous files to yourself and paying out the ass for it. Or you can just send things to your firstname.lastname@example.org account, which won't whisper its way to your Kindle until you're on wifi. Finally only approved email addresses can even send content in. True, it's very easy to spoof an email address, so I just created a very obscure email address name and use that as the only approved address.
Maybe that information will fill any gaps in what you've researched. It was all pretty confusing to me and I ended up just buying a book and having Whispernet give it to me over wifi to see if I was charged. Nope! As far as how much they charge? Well, that's one of those 'vote with your dollar' sort of things.
For my part, I owned a Nook and really didn't like it. When Kindle 3 came out I did a lot of reading. I didn't feel the need to buy the 3G since I can just flip it on in the morning at home and let it sync and then go about my day. I don't subscribe to periodicals, but even if I did I could set up a small script to hit up those websites and send it to my email@example.com account for free translation into their PDF format. And finally, well, I can't imagine (personally) sitting somewhere without access to wifi or a computer and thinking, "Shit! I need to buy and read a book RIGHT NOW!!" And if I do? Odds are my phone is around.