Honestly, I see Cera as no worse than Littlefoot in the movie. Sure, at first, she would rather be alone and chased away Littlefoot, but what did Littlefoot do when he first met Ducky? Tried to chase her away, until he learned she was alone too.
Cera did give up on the idea of being alone when she found out Sharptooth was alive, which is normal behavior, but that did not make her an angel. Same thing with Littlefoot. Yes, he did act nicer in comparison to Cera, but that doesn't make him so much better; he still acted bossier than Cera and he still, as CT pointed out, used Ducky as bait rather than himself.
Cera, despite her bad demeanor, never once did this. When she and Littlefoot were attacked by Sharptooth for the first time, Cera never shoved Littlefoot into Sharptooth's path. While they were being chased by Sharptooth later, she never tripped anyone to save herself. In short, she never tried to endanger anyone's lives for her own benefit, whereas Littlefoot did just that so he could take down Sharptooth.
Both Cera and Littlefoot made mistakes. But they are no worse than each other. I see Cera as no more bad or guilty than Littlefoot and vice versa.
Yes you could say Cera is worse in the sense of leading them into a tar pit near a volcano and they almost got killed, but then so did Littlefoot. Yeah he didn't lead them into such an area, but he did lead them into danger; climbing up that mountain face was dangerous, with one wrong move they could have slipped and gotten seriously injured, or killed.
Giving Cera a chance to lead did make sense, when you look at it logically. Littlefoot has yet to prove himself a capable leader. He has no proof the way he's going is the right one. After so long of no results, it made sense for the others to want to give Cera a try, to see how good she could do at leadership.
Also, Petrie wasn't trying to be insulting when he called Littlefoot "Flathead". The first time, it sounded like he was joking with him, which shows he felt comfortable enough around Littlefoot to joke with words that one would otherwise find insulting. He didn't look like he intended ill will towards Littlefoot.
And then when he calls him "Flathead" again when Littlefoot leaves after the fight with Cera, if you listen to the tone of his voice, it's desperation. Petrie is not joking now; he doesn't want Littlefoot to leave. The way I can make it out, Petrie just wants Littlefoot to be reasonable and not storm off like that. He doesn't want Littlefoot to be mad at them.