Because there is a really bizarre relationship in peoples minds between what bikes are fast and who rides them. For instance, Cervelo rode the CSC success and Cancellara's world time trial championships to the perception, perhaps correctly, that they made the fastest bikes in the world. They went from being a fairly small, well-regarded company to an industry 500-pound gorilla. What did that have to do with triathlon? Nothing.
Bike manufacturers don't want to cut off a percentage of their total sales if they can help it (i.e. the bike racers). Plus, none of the independents like Softride were able to definatively prove a non-UCI compliant design was faster.
I suspect that if the UCI becomes too stringent, then an independent is going come up with something faster, but again will have to overcome the perceptions of the unsophisticated to get the masses to buy it.