As much as anything, it's the negative feeling that it engenders. Unless they do something really stupid like making private repos accessible to M$ 'for usage statistics' etc then there's not much they can do.
Well, they can force ads for starters and insist on "user tracking" perhaps. Possibly even wanting a % of any code ownership. This is MS we're talking about and they WILL find a way to monetize it to their benefit at a cost to everyone else, A benevolent despot they are not. I'd very much be afraid.. very afraid.