They probably do need to lighten up but I can see their point here. Ellen's poking fun at herself but Apple's afraid it will translate into "the iPhone is hard to use". Apple's now looking to target the Computer Illiterate folks and the fake commercial could be seen as a sign that it's hard to use. Which is why Colbert and Stewart (who mocked the company and not a specific product) didn't get calls.
It's reactionary but not illogical.