This module works fine for me, Ubercart 1.0, Ratequote 1.01 with the shipping percentage patch, and the new uc_ratequote_configuration() {not sure if it made a difference).

EDIT:

If anyone is looking for an easy way to do BOTH flat rate AND a percentage fee, after applying the patch, open uc_ratequote.module and starting at line 287 comment out the if/else statements and add "$rate + " to the front of the $rate = declaration.

CODE (bold text is what is not commented):
# if ($rate > 0) {
# $quotes[] = array('rate' => $rate, 'format' => uc_currency_format($rate), 'option_label' => $method['ratequote']['quote']['accessorials'][0]);
# } else {
# $rate = $total * ($percent / 100);
$rate = $rate + ( $total * ($percent / 100) );
$quotes[] = array('rate' => $rate, 'format' => uc_currency_format($rate), 'option_label' => $method['ratequote']['quote']['accessorials'][0]);
# }