Some passengers feared the suspect could have held everyone onboard hostage and felt the police should have let them off.
Others say that the police were just doing their job, and apparently they did it right, because the suspect was apprehended.
While Mayor Bloomberg and Police Commissioner Ray Kelly empathized with the terrified passengers, they defended the officers' actions.
"Opening up all the doors and letting everyone run in every direction and having a murderer back out on the streets doesn't make a lot of sense to me," said Mayor Bloomberg.
"It had to be a very harrowing experience. But, in terms of police response I think it was totally appropriate," said NYPD Commissioner Ray Kelly.
Immediately after the stabbing, someone pulled the emergency cord and the train screeched to a halt between Manhattan's Rockefeller Center and the next stop further north. Police said the 37-year-old Sanchez pried open the doors and dropped the knife on the tracks.
Just minutes later, the train was moving again as the engineer radioed ahead, and police met the train when it pulled into the station at 53rd Street. Sanchez was arrested as he stood over the body, Commissioner Kelly said Monday. The arrest took just minutes. No one else was injured.
Sanchez pleaded not guilty to charges of murder. His Legal Aid attorney did not immediately return a call seeking comment. His brother, Louis Sanchez, told reporters that the family was struggling to understand what happened.
"He's a family man, he's not a beast," the brother told reporters after the arraignment Sunday.
Johnson, 36, died at the scene. Little was known about him, and there was no number at the address provided by police.
Bloomberg noted the subways are safer than ever, and there had not been a slaying in the subway system this year.
"I have empathy for everybody that is in danger," the mayor said of the passengers on the train with the suspect. "The truth of the matter is our subways are very, very safe," he said.
About 5.2 million people ride the New York City subway every day.