I feel like this is too obvious even to ask (or that it is a dupe...) but here goes:
If we do not use already ground medicine on Shabbos for fear that we might come to grind medicine, then why can we use already ground salt and pepper on our food (assuming we can) even though each of those is ground up before use as well? Isn't it possible that we might come to grind more for the need?
The same holds true of other activities -- if we can't use a musical instrument for fear of makeh b'patish, why can we use a chair which might also need repair to be immediately useful? If we can't blow the shofar, shake the arba minim or read megillah for fear of carrying each, why do we read from the Torah, which also might have to be carried?