I believe there may be some bugs either in the Fontin font or in the fontspec package's method for loading this font. The following MWE shows that one can't get the "regular" ligated glyphs of Fontin Regular -- fi, fl, and ffi -- to show up properly. Interestingly, there is now such problem with either the "Ligatures=Tex" option or with any of these commands for the Fontin Sans Regular font. (In case this matters: I run TeXLive 2011 on an iMac operating under MacOSX 10.6.8.)
\documentclass{article}
\usepackage{fontspec}
%% ligatures in Fontin Regular: fi, fl, ffi
\newcommand{\ligstringa}{fish fly difficult}
%% additional ligated glyphs in Fontin Sans Regular: ff, ffl, fj
\newcommand{\ligstringb}{baffle shelfful fjord}
%% two common TeX Ligatures: -- (en-dash), --- (em-dash)
\newcommand{\ligstringt}{-- ---}
\begin{document}
\setmainfont [Ligatures = {Common,TeX}] {Fontin Regular}
\ligstringa \ligstringt
\setmainfont [Ligatures = {NoCommon}] {Fontin Regular}
\ligstringa \ligstringt
\setmainfont [Ligatures = {Common,TeX}] {Fontin Sans Regular}
\ligstringa \ligstringt ligstringb
\setmainfont [Ligatures = {NoCommon}] {Fontin Sans Regular}
\ligstringa \ligstringt \ligstringb
\end{document}
Similarly, I can't seem to get ligatures going in the Fontin Italic, Bold, and SmallCaps fonts either.
One more thing: when I open Fontin Regular in Apple's Pages program, I experience no problems getting the glyphs to turn on (and off). This makes me suspect that the problem may lie with xelatex than with the font itself.