Set-returning functions are not allowed in WHERE

any(array)

You can use PostgreSQL's any operator to directly test wether the row's id is in your array:

select  from message where id = any(array[1,2]);

select  from message where id = any('{1,2}'::bigint[]);  

(you can even simply write = any('{1,2}'), however expliciting the ::bigint[] will make PostgreSQL directly target the right type, instead of (perhaps, I'm not sure about it) casting it to a text[] then comparing each text element to a bigint id)

(see it in a fiddle)

While the array contains distinct elements:

SELECT *
FROM   unnest($1) id  -- use matching column name
JOIN   message USING (id);

Even a bit cheaper for big arrays as Postgres does not try to merge duplicate entries.

• Optimizing a Postgres query with a large IN

If you're using Spring, use JPA and code like this:

public interface MessageRepository extends JpaRepository {
    List findByIdIn(Collection ids);
}

You can read about JPA here.