The usual approach to dungeons is, toughest monsters at the bottom. The deeper you go, the worse the trouble.
Generally, because it's more fun that way. It's not going to be a good game if the dungeon's dragons and demon princes guard the door and the goblins hide in the back, even if that would make sense from another perspective. The baddest-ass monsters are down the furthest.
Here is a roundup of reasons (read: rationalizations) I've cooked up, found elsewhere, had suggested by my players or friends, or otherwise glommed on to. I'm not linking to sources because none of these really come from one specific place, they're more of general themes.
Why are they down so deep?
The dungeon keeps going until it reaches hell itself. Pretty self-explanatory. Stands to reason the really bad dudes are in hell. Maybe killing the ones up top just re-allocates them down to the hell levels as fodder there.
The dungeon is hell itself. The upper levels are just the upper reaches of hell. Serves you right for opening that door and going in.
The underground is where you hide from the eyes of God. Or "the gods." Or whatever. The deeper you go, the safer you are from the eyes of God. This works really well with pantheons of gods who live up on mountains, or in the sky. So the tough, evil monsters - the ones most to fear from a just and angry god - go down the deepest where they can do the most evil unmolested by god.
It got buried by time. Cthonian weirdness buried for millions of years is down there; it's all stuff that started on the surface but slowly got buried. It just hasn't (or doesn't want to) worked its way back up.
They fear the men and their light. Simply put, the more monsters fear light (or even fear contact with humans and humankind), the deeper they'll want to go.
They need the heat. Deep down in the earth the temperature goes up - perhaps the worst monsters are also those who most need the warmth of the dark depths.
I'm sure I missed some good reasons to put the tough monsters down deep instead of up by the huntable humans and their wealth. Please let me know in the comments.