What kind of sealant can I use on my spray painted freezer?
Most rust-proofing paints are fairly hard enamels, even if they are matte finish.  Unlike house paints, they are not supposed to chalk off. It is more likely that handling the matte finish might make it a bit shiny in places rather than the finish coming off on your hands.

There are some matte polyurethanes, but they may not be as hard as the finish you are already putting in it. There is an article here describing matte poly.

If you do try a poly over the enamel, do a test in an inconspicuous area first.

SUPPLEMENT:
It looks like Rustoleum makes a matte clear finish that could be simply spray painted over your other finish. Other brands may have similar products.  I would still do a test in an inconspicuous place.