you can see people even now give him backhanded compliments while mentioning his stubbornness and immaturity in the past (even Dusty mentioned it)
What Baker said was that he never objected to Homer's "hardheadedness" -- he said it would be an important factor in making Homer successful.
Confidence, believing in oneself -- some will call it arrogance -- is good at the highest competitive levels. Some people looked at Homer as a kid who should have been more deferential to adults. He's also smart, which can make some people defensive.
Unfortunately, there are those who have never forgiven him for not conforming to how they thought he should be. So now they bristle at his success.