It’s less about not liking flawed characters, given that all characters are flawed in one way or another, and more about not liking characters who are flawed in certain ways.
I think there are reasons to respect Mako in the second half of Book 1 — he’s highly protective of the people he cares about, he stands his ground for what he believes in but apologizes if he’s wrong, he’s inclined to put practical concerns over romantic concerns, and he’s willing to support Korra in her plans even if he doesn’t think they’re the best idea. The thing is that most of those are colored in fandom’s minds by his other flaws into something more negative than they’re intended to be. =/
Hmm, I definitely agree that some flaws hit harder than others (especially ones that people are more likely to encounter irl), but while I agree that of course Mako does have good qualities in the latter half, I think your anon is onto something about the pacing. A lot of the things that give Mako the most audience sympathy seem concentrated in the first half, and as far as I can tell he was generally well-liked at that point.
Mako the prickly, formerly homeless gangster, currently plucky pro-bender desperately trying to keep himself and his brother afloat, and adorkably falling for the Avatar was highly sympathetic to audiences. But his efforts to retain their home and support themselves become unnecessary after the attack on the arena, his personal ambition vanishes in the wake of the revolution, the gang subplot disappears, and we hear nothing more about his and Bolin’s childhood. There are perfectly good reasons for these things in terms of the overarching plot, but that imbalance is still there—and I think particularly crucial because the only Mako subplot that really persists is the romance, in which he takes the highly unsympathetic role of “guy who waffles between two awesome, beautiful women, making everyone unhappy.” (And the show ensures that nobody forgets by panning to Asami’s suspicious/upset/angry face.)
It seems that his good qualities—which, yes, definitely are still shown—are shown mostly in the context of Korra’s love interest, which is a context in which much of the audience is already pissed off at him. So I think many people coming away with a disproportionately negative impression of him—which clearly did occur—can’t simply be blamed on audience misapprehension but on the structure of his arc, whether one considers that structure necessary or not.
Compare Tarrlok, who rapidly went from probably the most hated character on the entire show to fandom woobie. Even though he was a dick for most of the season, the sympathetic aspects of his characterization were mostly concentrated in the last few episodes, in highly dramatic ways, and so by the end, his sympathetic qualities were naturally in the forefront of many people’s minds.