Shoe Carnival at EWR
I am in EWR just about every week, either traveling or escorting my son through security, usually Terminal C. We are ALWAYS, without fail, asked to remove our shoes -- sneakers -- flip flops. The one time I was wearing thin rubber flip flops and refused, I was sent to secondary, despite not setting off the alarms.
It may not be the TSA's policy, but it certainly is in Terminal C.