They have done research into this and found several answers.
The food was not good quality and kind of Chinzy. The franchises were not able to give the specials like the $5 footlongs so the non-kosher customers would go in and get upset that the prices were too high and were confused why they could not order cheese on their roast beef sandwiches . The franchiese were forced to pay for ad campaigns that they could not participate in and get benefit for so they lost money on that.
Subways did alot better (and still survive) in places where there were less kosher options and did not get non-kosher customers (Like in JCC’s) in places like Cleveland