It's not amazingly obvious, but you can do flexible airports by putting in an area code or city that is between airports in to/from fields. i.e. if you do from:"palo alto" to:"salt lake", it will show flights leaving both SFO and SJC that go to SLC.
Something else interesting I noticed is that it seems to also return results for Amtrak.
Something else interesting I noticed is that it seems to also return results for Amtrak.