I'm actually watching the series again right now, so some of Sam's flaws are a little fresh in my head. The first flaw that really comes to mind is Sam's treatment of Al. Often when Sam disagrees with Al, he resorts to attacks on Al's character or past. Take for example, this exchange:
Al: You're gonna make nice-nice with the mother.
Sam: Well, it's worth a shot.
Al: I know that kind of woman, Sam. You're wasting your time.
Sam: Al, maybe if your mom thought she had a chance she would have come back.
-The Great Spontini
I don't see the above as representative of a flaw in Sam but, rather, a flaw in Al. Al often times will frame his view of something based on his past. In his past, his mother abandoned him and he tends to equate mothers as the bad guy in more than just this scenario. He does the same thing in the episode "Run Away" except, in that instance, a woman almost loses her life because Al's not willing to look past his own prejudice.
To me, Sam's biggest flaw is that he has to follow every single rule, unless following the rules means he can't make life better for himself or his loved ones (e.g. repairing Donna's relationship to get her over her abandonment issues, and everything in The Leap Home). It's a massive double standard, and I have to feel for Al - Sam wouldn't help him, but then wants to help himself in the very next leap doing exactly what he said shouldn't be done...
I think it's also safe to say that when Sam chooses to meddle in his own life, he is "punished". For example, he fixes Donna's abandonment issues in "Star Crossed" but did he really do her...or him...any favors. Sure, she doesn't feel abandoned by her father anymore. Instead, she's essentially been abandoned by her husband and he's not exactly living happily ever after with her. I'm not really sure where the improvement is there.
Also, just before he leaps out he questions whether GTFW is going to be angry with him for what he's done (or words to that effect), he leaps out and leaps into.....getting punched in the face. Either GTFW has a sense of humor or wasn't happy with what Sam had done.
The only thing we're really sure of from "The Leap Home" is that Tom isn't killed...but that comes at a price. Sam's left with the death of Maggie Dawson on his conscious. As far as whether or not his father still dies young or his sister marries an abusive alcoholic, that's something that's really not answered. I'd err on those parts of his past not changing...at least with regards to his father...based on the episode "Promised Land." When Sam talks with Al in the office he says something to the effect that they took the farm and it killed his father (again, I'm not 100% on what exactly was said). Al doesn't contradict that or look like he wants to but can't which leads one to believe that even after saving Tom, his family still lost the farm, and his father still died. It's not a stretch to assume that Katie still married Chuck.
Do you think that Sam has a tendency not to take Al seriously? Because of his libertine views of women, propensity towards sarcasm and easy-going disposition? After the hardship that Al has endured in his life - his unhappy childhood and his time in the Vietnam war - I'd say those are survival mechanisms.
No. I think there's a deep enough friendship between the two that Sam knows when to take what Al's say with a grain of salt (a lot of the stories about women) and when to listen to him. That relationship also enables him to point out to his friend when he's allowing his prejudice to shape how he's thinking and the opinions he's forming.
I think one of the best things about how QL was written is that both characters, Sam and Al, were written with their share of human flaws. This made them much more real and easier to relate to....and care about. Neither of them were really sainted martyrs, flawless and suffering for the other. I think examples can be found on both sides where one didn't place enough value in the other. I also believe that even more examples can be found of how each respected the other and that there was a deep friendship between the two.