For trombones, why does sheet music notation differ from the fundamental tone of the instrument?

Although the trombone's fundamental tone is B♭, unlike for a trumpet, the instrument's sheet music is always written for C. This is likely due to how the trombone came about.
Until the valve was invented in the early 19th century, many brass instruments were generally played around the natural harmonic. Players would switch out instruments to match the pitch of the music, or would even switch out the tuning slide for one of a different length to change the pitch of the instrument itself. It was therefore practical to use transposed sheet music. It is likely for this reason that trombone music is written this way.
However, trombones were capable of playing chromatic scales since around the 15th century, so actual note notation quickly became the general standard.
By the way, trumpets in an orchestra also use notation other than "in B♭ notation." There is also trombone sheet music in England written "in B♭ notation."