First of all, a flintlock is harder to shoot accurately because there is a longer delay between pulling the trigger and the main charge igniting. It requires more patience and a steadier hand to avoid reacting to the pan powder flash and thus spoiling the shot. Some people practice for years before they develop the ability to not 'flinch' when the pan powder goes off.
Second, the flintlock ignition sequence is inherently less reliable, requiring more attention to detail and care than the percussion cap. There is the hardness of the frizzen, the sharpness and continuity of the flint edge, the placement of the powder in the pan, the geometry of the touch hole with respect to the pan and flint, the size and in some cases shape (beveled or not) of the touch hole or vent liner, the volitility of the pan powder, the volitility of the main charge powder and the geometry of the combustion chamber. Finally one must tune the lock itself to provide sufficient sparks.
Managing all those variables in addition to the many things every black powder shooter must learn, such as the proper ball and patch size, the correct powder charge, the right size caps, how to measure powder and charge the gun, proper use and handling of a flask, etc., can be daunting.