Because my agency has killed the Doctor once and attempted to kill him on a few other occasions. Braxiatel is my political rival of many centuries. Lord Rassilon is my President. The only Time Lord I don't have a...complicated history with is Omega. And even he, as co-founder of my entire race, would be difficult to categorize as merely an ally.

As for the humans...they were companions of the Doctor and the sort of people who tend to travel with the Doctor are generally not my idea of a good ally. [They're too compassionate for Narvin's usual methods.]