functions.php

/**
 * Change the taxable amount for product with ID 25 to 5 dollars
 */
function change_wootax_taxable_price( $price, $is_checkout, $item_id ) {
  if ( $is_checkout && $item_id == 25 )  {
    return 5;
  } else {
    return $price;
  }
}

add_filter( 'wootax_taxable_price', 'change_wootax_taxable_price', 10, 3 );