One of the appeals of Spider-Man is the idea that the reader can see himself or herself in the character. He's not perfect, although the question of how flawed he should be gets to a delicate balance. If he has no flaws, he's difficult to relate to and kinda boring. If he has too many flaws, readers still aren't going to be see themselves in Peter, and they're not going to respect him. Writers might be tempted to go to one extreme, liking the character so much that they're unwilling to do anything that might tarnish him, or using the idea that he can make mistakes to justify narrative laziness.
It is worth noting that the best Spider-Man stories do feature him making mistakes and/ or alienating the people around him. His inaction gets his uncle killed. In the Master Planner saga, he blows off people at college, traumatizes his girlfriend, and causes a lot of property damage. His friends and family are often kidnapped, and in one story his girlfriend was killed, and he went on a rampage to get her back. In Kraven's Last Hunt, he was repulsed by Vermin before he was able to see the guy as a victim of trauma. In the Harry Osborn saga, he viewed Harry as beyond saving.
So, what's the right balance? And how much is it shaped by how long Peter Parker has been Spider-Man (IE- at what point, should he know better)?