A letter does not have to go to all of the colleges. Plus you can always ask for add'l recs if needed later in the process (but before you submit).
You get to choose which letters of recommendation attach to a Common App for a particular college. For example, you ask Ms. Smith, Mr. Wayne and Mr. Jones for recommendations and they file them online with the Common App. When you go to submit your application to Xavier University, which only wants 1 rec from a teacher, you choose which to submit. You could submit Mr. Wayne to Xavier, Mr. Jones to Slippery Rock, and Ms. Smith and Mr. Jones to Podunk U.