Build a data structure from the relational layout you have provided aggregating the Yes and No entries and then walk the resulting structure to print the desired results. For safety you could add some data validation.

use feature ":5.14";
use warnings FATAL => qw(all);
use strict;
use Data::Dump qw(dump pp);

my @l = split /\n/, << 'END'; 
Ubuntu,Warty,No
Ubuntu,Hoary,No
Ubuntu,Breezy,Yes
Ubuntu,Breazy,Yes
Fedora,Yarrow,Yes
Fedora,Stentz,No
Fedora,Yarrow,Yes
Fedora,Yarrow,Yes
Windows,XP PRO,Yes
Windows,XP PRO,Yes
Windows,XP Home,No
Windows,XP PRO,Yes
END

my $h;
for(@l)
 {my @w = split /,/;
  $h->{$w[0]}{$w[1]}{$w[2]}++;
 }

pp($h);

for     my $o(sort keys %$h)
 {for   my $r(sort keys %{$h->{$o}})
   {my %yn = %{$h->{$o}{$r}};
    my ($yes, $no) = ($yn{Yes}//0, $yn{No}//0);
    say "$o\t$r\t$yes\t$no";
   }
 }
[download]

Produces

{
  Fedora  => { Stentz => { No => 1 }, Yarrow => { Yes => 3 } },
  Ubuntu  => {
               Breazy => { Yes => 1 },
               Breezy => { Yes => 1 },
               Hoary  => { No => 1 },
               Warty  => { No => 1 },
             },
  Windows => { "XP Home" => { No => 1 }, "XP PRO" => { Yes => 3 } },
}
Fedora	Stentz	0	1
Fedora	Yarrow	3	0
Ubuntu	Breazy	1	0
Ubuntu	Breezy	1	0
Ubuntu	Hoary	0	1
Ubuntu	Warty	0	1
Windows	XP Home	0	1
Windows	XP PRO	3	0