For one, the other companies have other redeeming features: Microsoft has MSR, Google also does some research as well as a lot of open source stuff and IBM also does good research. Even Facebook contributes more to the community at large and the state of the art, as far as I know. All that Apple does is mostly produce overrated products in secrecy.

Apple is also very anti-freedom in the GNU sense, and have horrible policies on iOS and their app store. They really treat developers working on their platform poorly, and actively work against letting their customers have alternatives. (Jailbreaking shouldn't even be necessary!)

However, the really worst thing is how popular they are. Their draconian policies on iOS have pushed other companies--like Microsoft--to emulate that on their own problems; as far as I know, Windows Phone is almost as locked down as iOS. So Apple is at a weird confluence of evil and popular support, which is much more dangerous than evil by itself (this is why they are more worrisome than e.g. Oracle or even Microsoft). Their worst effect is cultural--making the nonsense around third-party iOS programs seem reasonable.

If Linux dominated the market, you would be free to use it however you like. If iOS dominated the market, you'd have to play by Apple's rules--getting a developer account, going through their review process... And even OS X is going in this direction--you have to deal with Apple to get your code signed, and there are no alternatives.

In a lot of ways, Apple is worse than Microsoft in its heyday; their only saving grace is their small market share--thankfully, Apple does not enjoy a monopoly anywhere or even a large share of the desktop market. Still, ignoring scale, they really are worse than Microsoft was; the scale is the reason they get away with all the things Microsoft couldn't (like standard web browsers or music players).