You would want to use the NOT EXISTS
operator along with passing the taxonomy slug, which tells the query not to include any of a chosen category from your custom taxonomy inside the loop.
To exclude all posts that are in the taxonomy “fruit” (regardless of fruit kind), here is the snippet:
$args = array(
'post_type' => 'post',
'tax_query' => array(
array(
'taxonomy' => 'fruit',
'operator' => 'NOT EXISTS'
)
)
);
$query = new WP_Query( $args );