The team itself is not self sustaining yet, and Al Fayed loses money every year. In fact, part of the 13 million transfer fee Fulham got for Saha went to fixing up the cottage instead of to new players. I guess the logic behind it, is that if they build a larger stadium and field a more competitive team, they will draw in more revenue. Its rough being a mid-table team and trying to compete for fans with the other London sides like Arsenal Chelsea and Spurs.
I would like to stay at the Cottage as well, but their plans to make the cottage larger were shot down by the local government.