Jack had a good heart. Overall he was a really good guy. He had an irritating trait however. He was a bit too patronizing toward everyone. Doctors can be that way I guess. they are in the business of telling people how to live, what to do. they hold superior knowledge in their fields, and are smarter than average. They are used to being authorities. And they are used to people looking to them for answers, for medical issues anyway.

But Jack (and Locke for that matter) assumed more authority than just being the medical expert. When it was clear that Ethan was dangerous and was threatening to murder the survivors, Jack would not let anyone have a handgun. After the survivors had been attacked several times, after Claire had been kidnapped and another person murdered by Ethan, Jack still insisted on keeping all the handguns under his care, even though it was clear to him that there were several people in the group who were proficient in the use of handguns.

Obviously this was just stupid. He sacrificed the safety of the group to his need to control everything, even after he knew there were others on the island willing to kidnap and murder the survivors. Kind of like he was saying "no, I won't let competent people guard and protect the group, because I want to control the guns myself". He didn't even keep them handy so he could dispense them quickly if an emergency arose. He had them locked in the case and buried in the jungle.

Still, he wasn't as bad as Locke. Locke was the worst at this. He and Jack butted heads over this issue, who was going to be in charge.