Unloading horse from a minecart!

Solution 1:

1. Mine the Rail underneath the horse in the minecart. (So that it won't move.)
2. Put your cursor in position so that it is in the lower part of the minecart.
3. Mine away!

Solution 2:

i'm a few months late, but just in case someone else needs an answer to the same question: http://minecraft.gamepedia.com/Activator_Rail

alternatively, if you're playing a desktop edition, make a creative test world (because i haven't tried this), put a mob or an animal into a minecart and type a kill command with a @type selector set to target minecarts. if the passenger isn't killed too, go to your main world and fix things that way.