Other than having a huge, unmaintainable regex I don't really see your problem here. It matches fine for me:

#!/usr/bin/env perl 
use strict;
use warnings;
use Test::More tests => 2;

like ('$', qr/[\~]+|[\!]+|[\@]+|[\#]+|[\%]+|[\&]+|[\-]+|[\_]+|[\:]+|[\
+;]+|[\']+|[\"]+|[\<]+|[\>]+|[\,]+|[\.]+|[\\]+|[\+]+|[\*]+|[\?]+|[\^]+
+|[\$]+|[\{]+|[\}]+|[\(]+|[\)]+|[\|]+|[\/]+|[\]]+|[\[]+|[\t]+/, 'Massi
+ve regex');
like ('$', qr/\$/, 'Tiny regex');
[download]

Can you be a bit more detailed about where the problem lies (and why you're trying to escape these characters in the first place)? If you can do so in the form of a test like the above that would be really clear.