I just got off the Silver Star yesterday, and my close friends travel it regularly.
Winter Park is by fair the nicest area to get off in. However, it is an unstaffed station. No baggage check, and no assistance. Winter Park is the only one of the 3 that is NOT handicapped accessible. It is a long way to Disney from Winter Park.
Orlando is in an older part of downtown. Amtrak considers Orlando to be the "Walt Disney World area" station. There is a Hertz rental car desk in the station. Florida Vanpool provides transportation, amd Mears Transportation's "Motor Shuttle" is available from the Orlando station. Orlando is in a relatively safe area of town, but Kissimmee and Winter Park are safer areas in comparison.
Kissimmee is very small, but it is staffed. Baggage and ticketing is available. Cab or town car service is the only option in Kissimmee.
I personally prefer Orlando because of the station and shuttle services to Disney. I did not wait outside in Orlando though. Stay in well lit areas if you are outside.