The idea is presumably to force the association to prevent "troublemakers" from entering the stadium. Based on the list of decisions [1], some kind of disruption during matches seems to be common. And if the decision in Sierra Leone v. Liberia ("one match without spectators / CHF 50,000 / warning") is any indication, they'd prefer it if nobody watches at all.
Apart from being the only feasible option (how would you fine a crowd?) the idea is to make supporters think twice about doing stuff that will end up fucking over their team.
Obviously doesn't work as well if the sanctioned actions are political and not your average lighting bengals and throwing stuff at the ref...
[1] https://img.fifa.com/image/upload/mojmlrcxqpjdy4f4dksq.pdf