The rejections I have had have almost universally been for reasons that would benefit the end user. For example, one app we submitted used background GPS to track your running route. Apple told us we had to very clearly warn the user that it could impact their battery life. Another was a game that still had some placeholder art being used for achievements, Apple told us to resubmit with final art assets.
Their system is far from perfect, but after lots of rejections I can see its value.