It's not necessarily based on logic or reason. It's based on politics and circumstance.

MDMA became popular in the club scene during Reagan's escalation of the War on Drugs, before it had been firmly established as a therapeutic drug. Basically, it escaped the therapist's office too quickly and too intensely. There were a number of high profile deaths that occured due to co-ingestion of other drugs, excessive MDMA doses, and hyperthermia in hot, crowded clubs.

Ketamine was firmly established as a very safe surgical anesthetic before it escaped the operating room and became a recreational drug. It does have a better safety profile than MDMA, in that extreme overdoses are less likely to kill the person as they would with MDMA. It's also cost prohibitive to manufacture illicitly, so the black market supply is mostly diverted pharmaceutical supply. Because of these factors, there's been much fewer high profile ketamine deaths.

All that said, there are some valid arguments to be made from a safety and abuse potential perspective.