While it's possible, it requires a bit too much tinfoil for me to believe that Amazon would lose money on the sale of RPG books to drive FLGS out of business, given how small potatoes RPG books are for them overall.
A large retailer can use several methods to keep afloat while engaging in predatory pricing.
The easiest for a multinational is to sell at a slightly higher price in most of its markets, while simultaneously dropping its prices in the market its trying hardest to monopolize.
Example: I have heard, but cannot confirm, that prices at some online retailers in Canada are higher than can be accounted for due to the exchange rate between the Canadian and US dollars. I haven't heard about such differences in other countries.
Assuming again that Amazon is being an economic bully, it isn't neccessarily the RPG market that Amazon is trying to dominate. One other thing that FLGSs do better (or at least, more often) than online retailers is get access to certain specialty products. There is a Horrorclix Cthulhu mini you can only win by entering tournaments- most of which are sponsored by game stores, for example.
There are also sci-fi/fantasy/horror memorabilia that only show up in those stores as well- autographed books, limited run special editions, animation cells, movie props, etc., sometimes even special promotional items and tickets connected to movie premiers. Amazon and the others don't get those (at least, not first hand)- game stores do.
But the fewer game stores there are, the more access Amazon and others would have to those specialty items...