I used tax_query instead of tag__not_in and it works now.
if ( is_post_type_archive( 'event' ) ) {
$taxquery = array(
array(
'taxonomy' => 'event-tag',
'field' => 'id',
'terms' => array( 53 ), //the ID of the event tag
'operator'=> 'NOT IN'
)
);
$query->set('tax_query', $taxquery);
return;
}