I think above all, Petrie's defense of him is from his perspective of him: A noble hero could do no wrong.
It would be kind of like a parent thinking their child was a perfect little angel, and absolutely refuses to believe the teacher when they say that they stole from other kids, acted violently in class, and completely disregards everything he is asked to do. "Nooo, Timmy's a little darling! He would never do thaaaat!"...when in fact he does do all those things.
A big part of it is that Petrie loves him, beyond the fact that he acts like he has been a big hero, but because he's family. A lot of people would be in denial if they found out their relatives had a secret bad side...or just a side that was unexpected. When you love someone, you turn a blind eye to their dark sides or try to believe that they don't exist.
Critical thinking hoooooo!
Petrie's defense of Pterano pales in comparison to Littlefoot's strange unceasing defense of Chomper in films II and V. One might think, Chomper is nice. Well, yeah, but consider this, Chomper is the very same species that killed Litltefoot's mother. Chomper's parents tried to eat Littlefoot.
Littlefoot had no idea whatsoever what Chomper had been up to for the years in between films II and V. For all we knew, he could have forgotten the gang and gone off eating leaf eaters.
In fact, the fact that he doesn't call off chasing them in V until they are cornered and the look he gives them seconds before recognizing them is
very disturbing. Strangely, none of the Gang of Five asked why he chased them (why not call out "Hey it's me!" if that chase was more of an innocent nature?) in that canyon. (Also, the cowering nature of them when chased by a Sharptooth shadow is quite pathetic. If you're gonna die, don't make it so easy for your will-be-killer! Goodness!

)
Also, Cera's paranoia isn't totally off base. Chomper did start to succumb to his nature and bit her in the tail in II. Even Ducky and Petrie, normally very trusting characters, express doubts over Chomper both in II and V.
But, even though Littlefoot actually sang about his mother hours before meeting Chomper the second time, he never seems to think "Gee, I'd better be careful around this Sharptooth or else I could go the same way as her."
He doesn't even feel odd that Chomper's very naive belief that his parents won't eat them (which, in fact, turns out to be so false that his parents, if one looks into it enough, would eat any friend of Chomper, even another Shartptooth or Tyrannosuarus, based on what they said.) nearly got them caught by Chomper's hungry parents. Also, as Chomper has said that he and his family have had little food, he never seems to think "Hmmmm, maybe he is leading us into a trap. He and his parents would split us. I don't know Chomper that well and only knew him for a day. We've been apart for years. Can I trust him?".
Yes, Chomper turned out to be nice (unless he changes in some future film or in some future part of the TV Series), but, so, for that matter did Pterano as he saved Ducky (and, let's face it, she woulda needed saving anyway, as, if Pterano hadn't kidnapped her, Rinkus and Sierra most certainly would have themselves!!!!) (Also, we don't know if Pterano is good or if he'll go back to being bad in the future either.)
Also, let's face it from Pterano's perspective. He's banished for life. He won't ever be able to see Petrie unless Petrie leaves the Great Valley. He may believe that this Stone of Cold Fire is his ticket to seeing his nephew again. With it, he can overrule Grandpa Longneck and Topps and get back in and also use its power to be the herd leader he wasn't able to be before.
Unlike Pterano, however, Rinkus and Sierra would no doubt use it to enslave the Great Valley and kill anyone who gets in their way. Sierra's comment of "Once we take over, the first thing I'm gonna do is feed them overgrown eggs (i.e. the Gang of Five) to the Sharpteeth!" is stark proof of that. Pterano tells off Sierra for this and appears to care for the kids, even Ducky.
Also, Pterano saves Ducky in the end. After looking at the film and entries on it, I'd say Pterano is more anti-hero than villain and indeed the REAL villains are Rinkus and Sierra, the Evil Duo, whose fate, like Ozzy & Strut and Dil & Ichy, is unknown.
As for whatever happened to Petrie's father, I think it quite likely he may have followed his brother in law. It would explain why Mama Flyer is so mistrustful of him and wouldn't tell Petrie what had happened (and still hasn't fully). On the other hand, Pterano is her brother still, and, I think the idea of her strangling him, as some suggest, if her mate was one of Pterano's lost followers, is too much.
Littlefoot and Petrie aren't the only ones with strange trusting habits. Ali believed all of Rhett's lies until shown with solid evidence right in front of her that they were just that, lies.