They WERE running low on ammo, just before they took the prison.
Remember, though, that once they got a toehold, they talked about a number of tasks, including finding the prison armory.
That's where the automatic rifles (Maggie's M4) came from is my guess, along with the ammo to feed them, along with the tear gas, smoke, and flash bang grenades.
If the prison armory wasn't too badly cleaned out, they should be able to hold their own against the Governor.