You're right in that you will never know, but I really have to believe it was just an odd coincidence. Beyond the financial benefits of Amazon lending their name to Chase bank for the marketing of that card, I'm sure Amazon is clueless, hands off, and have NO involvement with transactions made with that card.
I've long been a fan of the convenience, security and rewards programs of using credit cards. I basically carry a little cash for the odd mom and pop store that I might run across the doesn't take plastic, other than that, I charge everything and pay my balances off monthly. I've earned more cash back, free gas, and free hotel stays than I can count. :)
Kingbee is right, not sure about the 10% figure, that sounds awfully high, but I think a 2 to 4% fee is typically what a merchant pays on a transaction. Using cards so often, I'll occasionally run across the unexplainable card denial, most of the time I blow it off and just use a different card...more often than not, it self corrects. I've had cards declined, then use the same card less than an hour later at a store down the street.
It's part of why I NEVER rely solely on one card. I also make it a habit that when traveling on an extended trip to make sure I have a couple of cards and that my wife has one or two cards that I'm not carrying and vise versa. That way, if I lose my wallet or she loses her purse, I'm not having to cancel everything and find myself stranded without plastic.