No - you have to use the Windows version. You can use that under Cygwin by adding -unix as the first switch after "ifort" - this will cause forward slash to be interpreted as a directory separator.
While I prefer to run ifort for Windows with the cygwin shells and x server, this doesn't mean that ifort is installed "under cygwin." Ifort still requires the Microsoft link (which must be specified in ifort.cfg), along with Microsoft run-time libraries. Both the 32- and 64-bit installations (under XP64) work this way.
