Works fine here:

my $html = 'this is the user text: «<!--usertext-->»';
my $userinput = 'Some text :)';
$html =~ s/<!--usertext-->/$userinput/is;
print $html, $/;
__END__
this is the user text: «Some text :)»
[download]

What you describe usually happens when you try it the other way round, ie treat $userinput as a regex. Then you should use quotemeta or m/\Q$userinput\E/ instead.

Also consider using a real template system like HTML::Template or HTML::Template::Compiled, and escaping "evil" characters like <>"& in your user input before you send it back to the browser. Both template engines also offer the default_escape option which you can set to "HTML", then you never worry about such things again.