You can, and should, have a Mass said for your Protestant friend, or anyone for that matter.
If the one we are praying for is in heaven, he is not in need of our prayers. If he is in hell, no prayer can benefit him. But because the Church does not presume to know if any particular soul is damned, we are not to judge but to pray. The rest is up to God. Only God judges the heart (cf. 1 Sm 16:7).