I don't think there are many companies who have the depth of info security knowledge that Github can draw upon. You might believe that running your own server and locking it down to your local network (as best your team can do that) is better, but I'd rather trust Github even if that means my code is available online. While the chance of being victim to a non-specific attack is far higher (Github is a much bigger target; I'm affected if they're attacked), the chance of someone targeting my code and actually getting it are far, far lower because Github is better at making things secure than I am, and they have people who are paid to make sure things stay that way.
A policy of only having your code on Github has it's flaws but making sure it's secure isn't one of them.