Can't comment much on Apple. But as a Muslim I've seen this in quite a few places. Both in India and the US.
It's not even that much a company thing as much as it is a personal thing. Some people are just bigoted and don't like you. In fact the very sight of your existence disturbs them very deeply. And yeah, if you are better than them, it just makes the problem more worse. It's like they have to now deal with the realization deep down that they inferior to the person they hate.
Mostly Muslims just move on, because we have bills to pay, and families to support. Over long periods of time, it's not really possible to fight these political battles every time you have bigots around you.
I've also known cases when things are proven beyond doubt and the HR is likely to take action on the bigot, they start citing excuses like 'mental health' and 'personal preferences'.
You can't win this, there are going to be these kind of people anywhere you go. You just leave them to their state, and move on.
I've even gotten cold stares for using the office budgets for books, Why do people like you have to read books and get better than us?
Many times it's subtle, but some people are just living through bigotry day in and out. They just can't stand you. And it becomes visible easily.