It's not for sure but highly likely that Microsoft will do some things that are not desirable. From now on, should you believe trending repos are not filtered by Microsoft? Don't you think they might put some advertisement for their own projects / products? What will they do with the massive amount of data they have now access to, including private repositories?

Those saying there is no reason to worry are just hoping for big amount of luck. Yeah I hope so too, but let's face it, it's very unlikely they're not gonna do anything undesirable and only improve the platform.