On FAT or FAT32 filesystems, files are always readable, and Cygwin uses the DOS read-only attribute to determine if they are writable. Files are considered to be executable if the filename ends with .bat, .com or .exe, or if its content starts with #!. Consequently chmod can only affect the "w" mode, it silently ignores actions involving the other modes. This means that ls -l needs to open and read files. It can thus be relatively slow.
On NTFS, file permissions are evaluated using the Access Control
Lists (ACLs) attached to a file. This can be switched off by using the
"noacl" option to the respective mount point in the
file. For more information on file permissions, see
the section called “Using Windows security in Cygwin”.
On NFS shares, file permissions are exactly the POSIX permissions transmitted from the server using the NFSv3 protocol, if the NFS client is the one from Microsoft's "Services For Unix", or the one built into Windows Vista or later.
Only the user and group ownership is not necessarily correct.