Deleting a Trip is one of the few things you can delete in GTFS Manager and still be afforded an Undo. However, if you Save your changes, you will lose the ability to Undo.
There are two ways to delete a Trip.
Delete a Trip Using the Delete Key
Highlight a Trip in either Schedule View and hit your keyboard's delete key. This will remove the Trip (and any Repeated Trips.)
Delete a Trip in the Edit Menu
Highlight a Trip and from the edit menu, select Delete Selected Trip