Any suggestions?
Of course, airport time needs to include the travel time to the Rome airport, the advance time to check in and go through security (I've only flown in to Rome, never out), the time to get from your plane in Milan to the bus to the train station and then, finally, the time on the bus from Malpensa to the train station in Milan. Which is where you would be if you simply took the train from Rome to Milan. Hands down, I'd take the train.
Alex,
The best way to travel from Rome to Milan is absolutely by train. Travel time from Roma Termini to Milano Centrale is 3.5 hours via EuroStar Italia / Alta Velocita and second class fare is currently listed at €89.
As Doug pointed out, for travel by air you'd need to allow time to & from each airport (and of course airport transportaton at each end), security, check-in and waiting times, not to mention restrictive baggage limits and possible extra charges for baggage over the limit. There's no way I'd travel by air on that route!
Cheers!