There's no direct train from Rome to Lake Como. You go through Milan โ which is fine, because it's fast and the connection is easy. Rome to Milan is 3 hours, then Milan to Varenna is another hour. Total: 4 hours, one change, zero stress.
Leg 1: Roma Termini โ Milano Centrale by Frecciarossa (2h55). Leg 2: Milano Centrale โ Varenna-Esino (1h, โฌ7.60 regional). Or Milano โ Como San Giovanni (38 min, โฌ4.80). Buy leg 1 early for โฌ29. Leg 2 is cheap regional โ buy at the station.
Long drive and unnecessary unless you plan to explore mountain roads. Parking in lakeside towns is a nightmare โ narrow streets, ZTL zones, โฌ20โ30/day in summer.
The ferry system is your best friend. Buy a daily pass (โฌ15 central zone) and hop between Varenna, Bellagio, Menaggio, Tremezzo, and Lenno.
Frecciarossa to Milan + regional to Varenna. Leave Rome by 8am, have lunch on the lake by 1pm. Don't drive โ you won't need a car on Lake Como.