Son went to the recent ABCA convention and there was an entire presentation on how to "get around" this issue by building in positions that have titles other than Assistant Coach.
It's a shame that they have to. It definitely takes more than two guys to run a successful baseball program at the college level. Many tasks are given to each but we're not just talking about hitting fungo's and coaching the bases.
Just off the top of my head, practice planning, recruiting, travel arrangements, compliance, equipment/uniform management, game scheduling, academic tracking/guidance, managing website and other media, scouting/game plan, game management, strength and conditioning, pitching programs, camp coordination, facility scheduling, trainer coordination, team physchologist/spiritual leader, fund raising, oh yeah, and actually coaching several hours a day. Besides, with only two, it definitely limits what is so important to the players - getting sufficient qualified individual instruction to maximize their abilities.
Administration levels are very thick at most colleges. Yeah, football brings in more money but it also costs way more and the players are all attending for free in most instances. Most baseball players are contributing tuition and room/board money to the university. The spend is warranted.