On Susan's Ryanair information, you don't fly from Rome to Venice. On Ryanair, you fly from Ciampino airport which is an hour bus ride from Rome and you fly into Treviso which is an hour bus or train ride from Venice. Considering Ryanair's checkin time rules, you won't save any time over the train.
As Frank explains above, the difference in travel times for this run is due to two circumstances. I see Alto Velocito (A) and Intercity (IC) trains. The A train takes 4hrs. 22min. The IC train takes 5hrs. 52min. The A train makes far fewer stops. The IC train is a lower category train and makes lots more stops. For the run you see with a train change in Bologna, there is a 30min layover between trains and the second train is a slower IC train.
Finally, the A train costs more than the IC train. The A train run costs 56.10Euro. The slower IC train run costs 41.50Euro. Same tracks, more stops.