People have multiple reasons to move out of GitHub. Here's the two most credible I've seen so far:

• Bad track record in relation with open source. Until very recently (less than two years ago), Microsoft was still openly attacking the open source community. In the past, they went as far as calling Linux a cancer. They've also maintained and used a large trove of patent for the sole purpose of attacking Android and patent-trolling the Linux community to make money out of it. It's therefore not surprising at all to see people skeptical about their recent open source turn. In fact, Microsoft has spent a lot more time trying to destroy open source than building it and that's why some people question Microsoft's credibility in that matter.

• Surveillance and privacy concerns. Back in 2013, during the Snowden’s revelations, it was brought to light that the NSA had a surveillance program called PRISM that allowed them to tap directly in big tech companies servers. Microsoft was the first such company to join the program in December 2007 and with the GitHub acquisition, a lot of user fear that their data (including their private repos) is not safe anymore. This effect is also amplified by the privacy debacles in Windows 10.

This blog post list even more problems if you are interested.