MRL

The initials on John's boot are three letters ("MRL") hidden on the bottom tread of the Master Chief's boot in Halo: Combat Evolved. They are, indeed, initials - those of Marcus R. Lehto, Halo's Art Director (and the man behind the Master Chief's skin and armor design).

Walkthrough
An easy way to see the initials is if you're on a reflective surface (e.g: on Two Betrayals, while on the Control Room's bridge) just look down on the floor and on the Master Chief's boot are the initials. Of course, the easiest way is to play co-operatively and have one player crouch while the other zooms in on their right foot with a pistol or sniper rifle.