Microsoft was also bundling. E.g. Internet Explorer. To its (very slight) credit, Apple doesn't ship the iPad with iBooks installed by default.

Their control of the App Store is perhaps more-problematic (Microsoft couldn't actually stop competitors from using those undocumented APIs, once discovered). But at the same time, Apple doesn't dominate the mobile market like what Microsoft had on the desktop. (Similarly --obligatory bad-car-analogy-- auto companies exercise far more control over their dealership networks than Microsoft ever did over its resellers. But the FTC/EU took issue with Microsoft because of its monopoly status.)

Also, there's always the inconsistent treatment of game consoles to consider. The FTC has never investigated a dominant console supplier for not allowing any app from any developer onto their console. And Apple's App Store is wide open when viewed through the lens of that market.