Short Answer: No, Chipotle is not owned by McDonald's.
Long Answer: Chipotle became a susidiary of McDonald's in 1999 when McDonald's acquired the controlling stake of the company. At one point, McDonald's owned shares accounting for approximately 87% of the voting power of Chipotle's common stock. In Chipotle's earlier stages, McDonald's helped Chipotle's operations by sharing its own distribution networks.
Currently, Mcdonald's no longer has anything to do with Chipotle Mexican Grill. They have divested completely from Chipotle.
Source: Joe Stupp, General Manager, Chipotle.com