Indiana Jones is an arse, and Belloq was misunderstood

1. An archaeologist finds the Cross of Coronado in some cave, and Indy immediately steals it so he can sell it to a museum. After a long chase where Indy trespasses onto and damages a train, the local sheriff returns the cross to its rightful owner who decides not to press charges against him. How does Indy respond? He steals the cross again several decades later and kills the owner and several others in the process. The owner clearly had a passion and love for the cross as evidenced by his boat's name.

2. Indy goes into a historic Mayan temple and steals a sacred statue while destroying the temple in the process. He steals the statue so he can sell it to his friend's museum. The Mayans are understandably pissed Indy stole their sacred statue and destroyed the temple.

3. Belloq returns the statue to the Mayans who still worship it instead of letting Indy keep it so he can sell it to his friend's museum. Later, it's shown that he's working with the Nazis to find the ark. So what? He treated prisoners well and didn't injure or kill anyone. He just wanted to find one of the greatest and most sacred artifacts in the world. So did Indy who had the chance to blow up the ark but chose not to. This makes Indy just as culpable to the Nazis as Belloq. He even exposed the Nazis to some Jewish culture before opening the ark. Maybe this lessened the anti-Semitism in some of the soldiers before they were all mercilessly killed shortly afterwards.

After all this, somehow Belloq the bad guy and Indy is the good guy.