With the current microtype from TeXlive 2011, you can do the following:
\documentclass{article}
\usepackage{fontspec,microtype}
\defaultfontfeatures{Ligatures=TeX, Scale=MatchLowercase}
\setmainfont[SmallCapsFeatures={LetterSpace=6}, Numbers={Proportional,OldStyle}]{Minion Pro}
\setsansfont[LetterSpace=3, Numbers={Proportional,OldStyle}]{Myriad Pro}
\SetProtrusion
[ name = min-eu2 ]
{ encoding = {EU2},
family = MinionPro }
{
{,} = { ,500},
- = { ,500}
}
\begin{document}
\hsize 3in
When, while the lovely valley teems with vapour around me, and the meridian sun strikes the upper surface of the impenetrable
foliage of my trees, and but a few stray gleams steal into the inner sanctuary, I throw myself down among the tall grass by the
trickling stream; and, as I lie close to the earth, a thousand unknown plants are noticed by me.
\end{document}
LuaTeX with fontspec uses EU2 encoding internally, so all you need to do is the regular microtype setup with encoding EU2.
Best Answer
You can look at the source code for the documentation here: http://mirrors.xmu.edu.cn/CTAN/macros/latex/contrib/microtype/microtype.dtx