Nah, Goombas are smart. Some of them just defected to Bowser's side after he decided to wage war on the Mushroom Kingdom. The problem is that they don't hold up well against humans, at least not Mario.
I also don't think the Goombas are as weak as people make them out to be. One needs to remember that Mario is super-strong. Maybe the Goombas can only be crushed by someone strong enough. After all, Goombario's head was supposedly as hard as a rock. They also have those sharp teeth, which would probably be painful to get bitten by. Lastly, you have to think of a Goomba's relative size. Mario is pretty short and a Goomba is about the same size as him when he's Small Mario, so how big is a Goomba compared to the average human?