Taking into account travel time to and from the airports, plus time spent in security, you might be looking at longer than 3.5 hours.
Still, travel along the Northeast corridor would be a lot cheaper if those fares didn't have to subside ridiculous cross-country routes. A one-way ticket from New York to Los Angeles (changing trains in Chicago) costs $266 and takes 62 hours, not including the 5 hour layover. Why are these trains still running?
There are relatively few people that take the cross-country trains end-to-end, and a lot of people that get on or off at some little town along the way. For many of the more rural parts of the country, this is their primary access to long-distance travel. (This is especially true since the various phases of airline deregulation have increasingly caused smaller airports to close.)
There are also strong network effects in play. NYP to BOS is great if you're just going from NYP to BOS. But if you're going from NYP up to Portland, or BOS to Trenton or Pittsburgh or something, the cheap NYP-BOS connection is useless to you unless there are also not-extremely-expensive links from NYP or BOS to your actual endpoints. Part of what makes NYP-BOS so cost-effective as a route is that it's also fed by other lines that A) exist and B) aren't prohibitively expensive.
A political reason is that the keep-Amtrak-alive coalition is basically a mixture of urban transit advocates and representatives from rural areas who want to keep their town's train stop. A system that only served the major cities wouldn't have broad enough support, especially if it were only the major coastal cities (e.g. if you cut the Chicago, St. Louis, Pittsburgh, etc. services).
Taking into account travel time to and from the airports, plus time spent in security, you might be looking at longer than 3.5 hours.
Still, travel along the Northeast corridor would be a lot cheaper if those fares didn't have to subside ridiculous cross-country routes. A one-way ticket from New York to Los Angeles (changing trains in Chicago) costs $266 and takes 62 hours, not including the 5 hour layover. Why are these trains still running?