I've done articles before comparing the Seattle to Portland travel options of driving vs. flying vs. the train. Although my initial impression was that driving would win on cost and flying would win on speed I was wrong. All three methods take the same amount of time from downtown to downtown if being fair (ie. you need to put gas in the car, get through security, wait in line to board the train etc..). The train ended up being cheapest for up to 3 people and by far the most enjoyable. Flying lost every comparison. When you fly you have less usable time, more interruptions (light rail, security gates, boarding, wireless disconnect, de-boarding, light rail) and more discomfort (small seat, TSA) so it lost in every aspect. The Amtrak Cascades won in most aspects outside of freedom once arriving at the destination and frequency.
The reason I'm writing about this again is that Hipmunk a travel search engine has added Amtrak to it's search results. What's also interesting about Hipmunk is that it includes an Agony filter. You can sort by least Agonizing trip. I'm not sure what criteria Hipmunk uses but I'll show the results for Seattle to Portland trips. Also keep an eye on the prices for a round trip ticket. The trip with the least agony is also the cheapest.