You cannot just create a superuser in cygwin because cygwin is a
translation layer for UNIX applications. Cygwin is not actual UNIX
and there are limitations. Basically cygwin is using the host
machine's security model rather than unix's own native security model
and porting is not straight forward for some applications. It is even
worse when it comes to WIndows 9x than with Windows NT where as 9x has
no security model of its own (that I am aware about). The passwd and
group files are there for compatibility and allows some applications
to work. At least that is my understanding.