Ah, the age old question. Are the Organization evil and why doesn't Sora stop to think otherwise?
Well - why should he? The first time he ran into them was after Yen Sid - someone obviously trust worthy going by Donald and Goofy's trust in him, told him the Organization were a thread. And what did they do? They attacked Hollow Bastion, filled with Sora's friends. They continued to harm the people near and dear to him, both in the Coliseum and in Beast's Castle. He ran into them when they attacked HB again, continued to terrorize the worlds, and then held one friend captive while withholding information about another friend, all the while taunting him about Riku being in mortal peril.
Screw their reasons, this isn't being misunderstood, this is being evil, and Sora had no reason to even try and see beyond it.
The irony is that had they talked to him, Sora probably would've helped them. Depopulizing the Heartless is a joint goal for the both of them, and turning Nobodies into Whole Beings sounds just like something Sora'd be interested in getting to. It certainly would make his life easier at least a little bit.
They didn't offer. They hurt the people he cared for, and they hurt him.
Why should he give them a second thought instead of launch at them with Keyblades blazing?