SMT PLT FELT TWR CLRED MLG FOR TKOF TOO SOON AFTER HIS LNDG.

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I WAS WORKING LC1 AT MCO TWR. SMT X WAS ON THE ILS APCH FOR RWY 36R AND TOLD TO RPT THE ARPT IN SIGHT FOR RWY 36L. HE RPTED THE ARPT IN SIGHT AND I CLRED HIM TO LAND RWY 36L. MLG Y WAS HOLDING SHORT OF RWY 36L AWAITING DEP AND WHEN SMT X CROSSED THE THRESHOLD; I INSTRUCTED HIM TO TAXI INTO POS AND HOLD. I OBSERVED SMT X CLRING THE RWY AT TXWY A-2 AND CLRED MLG Y FOR TKOF. 2 MINS LATER; SMT X QUESTIONED A DEP AND I SAID 'YES; I HAD ONE DEPART 2 MINS AGO.' HE SAID 'HE WENT RIGHT OVER THE TOP OF US.' I SAID 'IT APPEARED YOU WERE CLR OF THE RWY.' HE SAID 'NO; HE WASN'T.' WHEN MLG Y LANDED AT HIS DEST HE CALLED AND ASKED. HE STATED THE SAME SEQUENCE OF EVENTS AND SAID THAT SMT X WAS CLR OF THE RWY WHEN HE STARTED TO ROLL. THE VISIBILITY WAS POOR DUE TO RAIN AND FOG AND WITH ALL THE CONSTRUCTION LIGHTING ON THE W RAMP; I STARTED TO WONDER IF HE WAS ACTUALLY CLR. MLG Y WAS IN A MUCH BETTER POS TO SEE SMT X AND REASSURED ME THAT HE WAS. I ASSUME THE ENG NOISE JUST STARTLED HIM. I WAS ALSO TOLD THAT HE WAS GIVING THE APCH CTLR A HARD TIME AND WAS POSSIBLY UPSET ABOUT SOMETHING.