I'm just a humble PPL student so don't shoot me if this is bo*****s.
I'm sure other's will correct me and/or elaborate but I think the argument goes like this:
Commercial traffic fitted with TCAS would like to know the altitude of GA traffic for collision avoidance - and currently they can't if your aircraft is only fitted with a mode A transponder. This is what the aircraft I am learning to fly on is fitted with and my instructor has it turned to standby to avoid alarming the airliners passing overhead at a much higher altitude. I think they want GA aircraft to be fitted with altitude reporting mode S transponders.
I think GA's argument against them is that it is very costly to buy a mode S transponder and that it is unfair to expect GA to pay for it.