Well, one of the reasons is actually outlined in the article (read the last few paragraphs).

Also, apparently over-booking is a rather profitable practice for the airlines and if they are facing increased costs because of restrictions or higher payouts to bumped passengers, they will simply pass the costs on in higher ticket prices.  They will get the money and one way or another it is the passengers that will pay.

I'm not against a passengers bill of rights, but it is true that the cost of flying can be expected to go up as a result.