McDonald's bought into it early, expanded it, then spun it off as an IPO. They don't own a majority stake (if any of it) anymore.
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.