Historically, the Turkish military has been a sort of check on the democratically elected government. If the government gets too secular or gets packed with fundamentalists, they seize power and institute new elections.

When Erdogan got into power, he must have feared that his new fundamentalist policies might put him in danger so he tried to weaken the military leadership as much as possible. Looks like he didn't weaken it enough.

If history is repeating itself, and this succeeds, then this is a good thing for those in Turkey who are secular and love the cultural connections to Europe.