Now if the Ent-E is considered the flagship vessel, that might mean other Captain's might consider Picard as the most senior Captain, which is why they allowed him to take command of the fleet.
Like I said, the other captains allowed Picard to take command because they recognized his experience - both with the Borg and with pretty much everything else. Picard's record of service in Starfleet is well known. Everybody knows he's a good captain. So given that Starfleet was getting its ass kicked left and right, they were almost out of options. And then along comes Picard, who has years of experience with the Borg - something none of them have? Of course they're going to let him.