I recently took a trip from San Francisco to New York City to Boston and back to San Francisco. To arrange this I booked two airplane tickets separately, and one Amtrak ticket.
One of the greatest revolutions in travel planning took place when it became possible to easily search and book trips, including multi-stage ones, together at once. Had I made my trip entirely by air, I could have used the multi-city options at any one of the flight search engines. However, since I did not want to deal with going all the way back out to any of the notoriously inaccessible NYC airports, I chose Amtrak instead for convenience.
Hopefully in the near future, this kind of multi-stage trip planning will be extended to multi-modal trips as well. Perhaps with the advent of Google Flight as competition to Bing Travel, and the other preexisting engines, one of them will jump on this.