If your software works with fewer bugs, if you deliver faster than the competition, if you make customer returns incredibly simple, if you respect your customers time more than your competitors do, if your pricing is more up front and honest, if your customers choose you over your competitors, are you "unfairly" undercutting competitors.
Traditional monopolies were built by selling at a loss to force competitors out of business or to sell to you (think J.D. Rockefeller, who famously said, "competition is a sin." ) Amazon so far as we know, does not engage in any of these practices. It buys businesses at competitive prices that are not competitors at the time of acquisition. This practice allows Amazon to move into entirely new ventures. It competes by doing things better than the competition. Is that unfair?
Amazon is not trying to sell at lower prices than Walmart or at a loss, in an attempt to drive Walmart out of business, and it is not interested in buying Walmart. It competes with Walmart.com by doing things much better than Walmart.com does them! And it will eventually put Walmart.com out of business, unless Walmart changes the way it does business. Amazon buys, so far as I know, only non-competing businesses! Although Amazon was trying to make headway into the grocery business before it bought Whole Foods, no one in their right mind would, before the purchase of Whole Foods, have said that Whole Foods and Amazon were legitimate competitors.
I think Amazon will come through any FTC investigation, based on current statutory law, without much difficulty. Where they are more vulnerable would seem to be within the political arena. But I don't think they face much difficulty there either.
So long as Amazon has legitimate competitors in all its areas of operation I think it will easily withstand FTC scrutiny. The problem for Amazon is rather an ironic one. If it doesn't stop doing things so much better than the competition it may indeed eventually end up having a monopoly in one area or another. Then, through no fault of its own, Amazon may become an accidental monopoly.