Looks like it was creative differences. The show survived losing one runner and the show definitely improved under his running and ratings have showed the improvement. Interesting to see if this makes any difference.
ETA: To clarify, he will finish Season 3. Next season will be the new runner’s first.
A showrunner is the person who oversees the entire season (and usually series), so that different writers, directors, and actors etc, who come on board don’t derail anything too dramatically. They keep the style of the show and characters consistent. They will also sometimes rewrite scripts, uncredited, or come up with the story arcs. They’re usually the most important person on the crew for a TV series as they guide the whole shebang.
Resurrecting this because a replacement has been chosen: Scott Gimple who was a writer on several episodes. Also it looks like Mazzara’s leaving was not as amicable as previously reported…