(Scratches head)
I thought we were (at least at this point in the forum) discussing villainous forces as a group, not specific bad guys. It stemmed from San Holo's mention of ODESSA.
I was getting to the point that the group Indy's against has to be despicable and motivated by either greed or thirst for power. To make an (extreme) counter-example, let's say that Indy's trying to find a mystical artifact that is being pursued by an enemy culture that needs it to survive (for whatever reason). And this enemy group will do whatever it takes to acquire said MacGuffin.
So they're killing/kidnapping/hurting people, but without said MacGuffin, they'll die out. So by "graying" the audience interpretation of the intention and actions of said enemy group, the hero is seen as less than heroic. We want a certain "lift" by Indy bringing down the tyrannical bad guys, not sitting there wondering "is he even doing the right thing?"
Call it what you will, but the Indiana Jones films have always been about good vs. evil, and it's been pretty clear-cut who's who. Indy may fight dirty, but he's still the white knight in the saga.
There are varying degrees of evil, but Belloq, Mac, and Elsa all fit into that camp. Belloq places the artifact and acquisition of such above all things (to which Indy doesn't by placing Marion first). Mac's a traitor, to which Indy's patriotism and loyalty is beyond reproach. And Elsa, like Belloq, places the possession of the item above what it's supposed to represent; although she's not as bad as Belloq, she made the choice to ally with the Nazi party.
Again, trying to make the point that you can understand why the bad guys are doing what they're doing, but we're not supposed to identify or sympathize with them.