You fight your way through an army of cranky Germans, risk life and limb to rescue a priceless artifact of stunning religious significance, and those clowns in the government promptly bury it in the biggest warehouse they can find. Where we come from, we call that "irony." And certainly there's a bit of a Twilight Zone-y twist to it all, as the Ark everyone went through a whole movie to find ends up just as lost as it was in the beginning.

But beyond that twist—actually because of that twist—the ending's meant to show us that real prizes don't come with price tags. Indy may have lost the Ark, but he won some seriously good karma at the same time. Marion doesn't despise him anymore. He's done right by her and closed the gaping emotional wound he left her with when she was a kid. She's feeling better about her life, and may even want him in it if he doesn't revert to his previous Jerk Boyfriend form. In the big picture of this Big Picture, that matters more than any kind of magic object, no matter how holy or revered.

Granted, Indy can't quite let go of it; "they don't know what they've got there" is his last line in the film. But we can't blame him for feeling like that after everything he went through. At the end of the day, he does head off with Marion instead of running back in and demanding the Ark's location from the nearest bureaucrat he can find.

The irony, then, is not that the Ark remains lost regardless of Indy's efforts, but that Indy lost sight of the real prize until it was almost all over. That sounds a lot wiser than just "sorry, the government screwed you," and ensures that the ironic ending nonetheless remains a pretty darn happy one.