Chipotle is a national chain that is highly-profitable. Consider it the Starbucks of Mexican food. Not as good as the "local" place, but consistently okay everywhere you go.
They got involved because the first Chipotle was right near the McDonald's corporate offices in Denver -- the executives were eating there so much, they bought into the company!
Adding more weight to your point, I read that McDonald's divested their stake in the Chipotle chain, giving the reason that they wanted to focus on increasing revenue at their own restaurants.
