Microsoft now owns GitHub, npm, LinkedIn, the Office suite, & Exchange. They know who you work for, what you work on, what your development habits are, how and where you distribute your code (and to whom), and who you connect with. Remember, connections are not just made on LinkedIn. GitHub’s motto is “social coding”, not “code storage bucket”. This means Microsoft has the ability to produce insights into one of the most valuable/expensive workforces on earth.

Most people forget that the largest expense in running a business is the cost of labor. The company with the greatest insights into the workforce will have a competitive advantage.

Microsoft also gains some influence over the entire development community, which is something they used to have and lost over time. They initially tried to compete with GitHub, but failed. They became the largest contributor on GitHub, so it made sense to bring it in house and have the leaders be a part of Microsoft.

Update:
GitHub just bought npm, which aligns with the strategy described above. See Corey Butler's answer to Why is Microsoft buying NPM?