pg_dump is a logical backup, that is, as you've seen, it queries the all of the data in your database in writes to a file in the form of queries that will re-create all of your data in a new database. This great and very flexible, but as you've seen has some limitations.
You probably want to look into physical backups, where you basically copy the actual files that postgres is actually using to store your databases on disk (although it's not quite that simple, so do some googling on it). This has the nice advantage of not requiring you to run queries against your database to back it up. It also gives you a consistent point-in-time backup of your database.
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pg_dump is a logical backup, that is, as you've seen, it queries the all of the data in your database in writes to a file in the form of queries that will re-create all of your data in a new database. This great and very flexible, but as you've seen has some limitations.
You probably want to look into physical backups, where you basically copy the actual files that postgres is actually using to store your databases on disk (although it's not quite that simple, so do some googling on it). This has the nice advantage of not requiring you to run queries against your database to back it up. It also gives you a consistent point-in-time backup of your database.