This is the sort of case where HTML::TokeParser::Simple really is simple:

use strict;
use HTML::TokeParser::Simple;
use Getopt::Std;

my $Usage = "Usage: $0 -f word file.html > highlighted.html\n";

my %opts;
( getopts( 'f:', \%opts ) and $opts{f} and @ARGV == 1 )
    or die $Usage;

$opts{f} =~ tr/,/\|/;

# This applies a regex substitution to the text part
# and leaves the tags unmodified:

while ( my $token = $p->get_token ) {
    if ( $token->is_text ) {
        $_ = $token->as_is;
        s{($opts{$f})}{<b><u>$1</u></b>}g;
        print;
    }
    else {
        print $token->as_is;
    }
}
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(update: forgot to include the assignment to $_)