There's a lot of growth opportunities if you have >20m users.
Now that I’m a customer, it’s really ridiculous how badly their stuff is integrated. I mean, when I find myself wishing for the good old days of using Trac pre-1.0 because at least it fucking works and I don’t have to log in four times while working a ticket through code review and into a deployment. I mean Jesus Christ Atlassian, you're on version 6 and you can’t make SSO painless, and every time I type in a ticket number into an input field behaves differently.
Why hasn’t a competitor eaten their lunch yet?
If Github burnt a ton of cash to try and compete with Jira, ended up making a product that didn't attract enough people over at the same time as ignoring problems that users were already grumbling about, this could have led to them being in a worse state and easier for MS to pick up on the cheap.
Only recently did I discover you can download the CLI without installing XCode first. Saves about an hour off of setting up a new developer.
Equally, on their $200M revenue (or whatever it was), they would struggle to get a multiple that would be interesting for their VC backers. Their market cap at IPO wouldn't have been much more than $1B (absent some growth story).
It's a great problem to have, to be sure, but the MS purchase is a great deal for Github investors.