a)Across the nation is not always the most expensive. A low-traffic airport can be more. You were flying the major cross country routes...definitely not the most expensive.
b)Med schools don't always give you the luxury of 1-2months notice
c)They also don't let you choose which days of the week your trip falls on, which makes a huge difference in price
d)Anything near a holiday will be more expensive, period.
e)A $400+ trip can in no way be described as 'pretty cheap' anyway. It's still a significant expense even if it's less expensive than it could have been, and may not be worth it.
Yes, I've gotten great deals coast-to-coast...I'm headed from CA→VA for $267 round trip for my next interview. But that's called getting lucky; I'd never go try and tell somebody that just because I've gotten that deal for a cross-country flight, that's as much as they should expect to pay for theirs. You get unlucky as often as you get lucky, and sometimes you find the cheapest option for your interview, even months in advance, is $600+ on a crummy airline (yay Labor Day weekend scheduling!)