It is very difficult to play all FCS, because there just aren't enough teams available when UM has open dates. That's one of the reasons UM has to fill in with D2's.
And, FCS schools cost more money than D2 schools. This happens for 2 reasons. FCS schools demand higher game fees than D2's. Or, they demand home and home series. A home and home series reduces the number of games in Missoula, which reduces the revenue from home game tickets sales, etc.
FCS schools are farther away from Missoula and the cost of the charter is expensive. Many D2 schools bus to Missoula.
In some cases, UM may charge more per ticket for an FCS game than for a D2, but I'm not sure that is often the case. I haven't looked at ticket price comparisons in the last decade or so, so I don't know. Maybe someone else knows. I suppose an extra $10 per ticket brings in about 20,000 tickets sold times $10. So that would be about $200,000. I would guess that FCS one-game fees plus the cost of the charter would be more than $200,000 but don't know.
I think you are underestimating how much D2 games, with the teams coming by bus, and have lower game fees, save UM.