Here's what Stan wrote: 
Regarding instruments playing different notes - yes, some instruments are called transposing instruments; they play notes differently from the way they appear on the score.  That's why an orchestral score may have a line for "Trumpets in B-flat."  When those trumpeters see a C on the score, they actually play a B-flat.  To get them to play a C, the score has to show a D.
  
Trumpets (and other brass and reed instruments) come in different sizes.  The notes in the score tell the musician what fingering to use.  A trumpeter will use the same fingering to play C on a C trumpet as they would use to play B-flat on a B-flat trumpet.  But in both cases the score will be notated as C.
  
Of course, this is a hassle for composers, who have to think backwards to be able to get the right sounds from the musicians.  In fact, some 20th century composers finally said to heck with this, my score is going to show concert pitch for all instruments.  So for those scores the musicians have to figure out the transpositions themselves.
  
Now there's notation software which can handle transposition and make everyone's job a lot easier.  So my guess is, new music will probably continue the old practice of transposing.