We're just about to introduce iPads for all the pilots in our airline (about 3,700) and you would not believe the amount of compliance testing and general farting about that's required to get electronic equipment approved for use on the flight deck.
Apple makes two series of iPads (2 & 3). Take just one of those, iPad3 and you have various memory capacities with/without 3/4G. OK, standardise on just one model, say the iPad3 32GB 4G. This has batteries that come from several different manufacturers, not to mention GPS/wireless chipsets that are also sourced from multiple vendors. Each of these has to be tested separately for compliance and if any more changes happen during production you're back to testing again.
Your average non-Apple tablet has these problems as well, plus is much more of a moving target in terms of continually changing hardware. Many of the cheaper units would have difficulty during the approval process from a technical point-of-view (shielding, RF emissions, battery construction, etc.).
Most of the reason that iPads are fairly ubiquitous at the sharp end of commercial aircraft is not some pro-Apple bias but simply that a great deal of work has been done (and money spent) on certifying them for this, so you don't have to re-invent the wheel if you want to fit them in your aeroplanes...