I would guess it is many reasons - company tickets, free tickets, student tickets, or simply just season ticket holders that can't, or don't want to, go to the game. I imagine that there are folks that just buy season tickets out of tradition or habit, but only want to go to a few games. They keep renewing so they can keep their priority and their good seats when they do go.
Weather, conflicts, start times that don't work for them - but I'd bet the single biggest reason is ambivalence - people that are just not motivated to go.
This is why expanding the number of seats in stadiums like Kinnick makes no fiscal sense.