For the ends of bolts sticking out past the nuts; Home Depot has the plastic covers that are the same type of thread protector you see on equipment that is shipped. Sort of a prophylactic for the end of the bolt, except you don't unroll it, it's already stiff. They're cheap and come red.
Now the difficult part. Nobody there is going to be able to find them for you, except your faithful servant (that'd be me) is going to tell you where they are at. Go to the machine screw and bolt aisle. Just when you are at the end of the bolts, you will see some clear plastic, tip-out boxes, in a rack. There are cork and rubber plugs, as well as spacers, in the same display. They are in there-I forget what they call them, but you only have about forty little bins to look through. They just push on over the bolt end.
btw, if you're cutting off a too long bolt, it's a good idea to put an extra nut on it before you cut it off. After cutting to length, back the nut off, and that will clean up the end of the bolt and thread for you. You may schwanz some nuts doing it but, at least you'll have clean threads in the future for when you take the nut off and have to re-use it.
“Scientists are people who build the Brooklyn Bridge and then buy it.”
Wm. F. Buckley, Jr.