There is an attendance limit at each level for the maximum amount of supporters you can get for a game, regardless of the size of your stadium.

Providing you get the maximum support allowed for the level you will still get the 5% possession bonus, even though your stadium will not be filled to capacity.

I wondered about the level cap on supporters for a while, but it really does make perfect sense and is the right thing to do in this game. Capping the supporter level is a way to stop token buyers gaining a huge financial advantage at each level. If it wasn't there the finances available to players with large stadiums would be an unfair advantage to everyone else on the level, and would mean that the player with a big stadium would have more money available than they would be able to spend.

The limit is simply a way of maintaining a steady growth of a club up through the levels, and also keeping competition fair and appropriate to each level.