Yes; the Doctor (particularly in his Third and Fourth incarnations) was frequently exasperated with or disapproved of UNIT's approach, but he seemed quite content to work with them. Mind you, it was shown in 'The Sontaran Stratagem' / 'The Poison Sky' that the Tenth Doctor, post Time War, had a much more jaundiced view of UNIT, although this subsequently seems to have been patched up to an extent. (Possibly because he realised that if UNIT doesn't deal with extraterrestrial threats, then Torchwood does, with even messier results.)