The nominal reason, I'm sure, was to give FFC a chance to shoot a more dramatic scene w/better lighting in a train compartment than in an airplane. It also gave us a better shot of the bodyguard, who we see for the first time.

But there may have been logical reasons, too:

Jet aircraft were introduced into US commercial aviation only a few months before that scene (December '58). If Michael had wanted to fly to Miami, he' have to take a puddlejumper from Tahoe to Vegas, the nearest "real" airport, and from there take a (probable) prop plane to either Chicago, St. Louis or Kansas City, and thence to Miami. It'd be arduous in any event. And, with that many stops, a foe could have had ample opportunity to attack him (look what happened to Roth at Miami International). So, Michael might have felt safer on a train, in a private compartment, with only his bodyguard inside. The longer time for travel also might have given him more opportunity to think.

You're probably right about Tahoe not being an express stop, or any stop, on a swift passenger train at that time. But I'll bet that Reno was--and Reno's only 61 miles from Tahoe. Or, he could have driven to Sacramento, another probable express stop--104 miles from Tahoe. Not Vegas, though--it's 453 miles from Tahoe.