Of course they didn't have their instruments plugged in. Anyone who knows anything about sound production knows that the logistics of the Super Bowl aren't just difficult, they're legitimately impossible. The E Street Band is the greatest live band of all time, and they played to backing tracks too. It's what happens when you only have a commercial break window to set up a massive stage, get a bunch of people on the field, and rig a massive stadium for quality sound.
This. The ignorance being displayed by those condemning Flea and others is beyond irritating.