Bows seem to reload faster, are quieter, can kill in about 1 shot, can fire over walls, are more accurate (in trained hands), easier to hide with, easier to produce, and does't break/require much maintenance.
Muskets dont seem to be able to do this, and the only reason I can think of is making a loud sound that can "damage" morale.
Hi! A quick peek over at the Military History section of the FAQ yields these threads:
If early guns were so inaccurate and took so long to load, why did they so quickly replace crossbows, archers, and other earlier forms of projectile weaponry? by /u/Rittermeister
Why were primitive firearms used when bows and crossbows were better in every way? by /u/Valkine
While more can always be said on a given subject, I hope that this is enough to get you started!