I'm searching back in the mists of time, but I recall there was something about MTBE being a waste byproduct of the chemical industry and using it as a fuel oxygenator sort of killed two birds with one stone. Which reminds me of stories I heard about the east coast mafia who would (for a price) drive tankers of hazardous waste around the turnpikes with the spigot dripping until it's gone.
MTBE isn't a waste product. It has to be refined in a special process. The feed stream is a different "cut" from the cracking column, and one that really doesn't have as much commercial demand as others.