Most assistants leave and go to other schools often. It is rare that you keep a core of coaches together for long. Coaches have aspirations of head coaching, coordinators, etc. Why pay someone and lock in a big contract when you know they likely won't fill it. I think most are paid about where they deserve. The head coach takes the fall for anything that goes wrong or right for a program. It is their reputation on the line. When you talk about Florida, Alabama, etc you rarely mention the assistants. You always talk about CUM, CNS, etc.
It is true the assistants do a lot of work. But at the same time they are usually only responsible for a small piece of the big puzzle. That is why position coaches make the least, coordinators next, and then head coach. You get paid according to your responsibility and titles on the team. The position coaches and some coordinators are expandable on most teams so they paid. It is the same when you go to a company and the head person gets paid the most but may do the least. The entry level jobs get paid the least but have the most work. It is all about working you way up and proving you can do the small work.