How to use not in in drupal views 3
My suggestion: You could make this a great deal easier for yourself if "Has payed" a field on the User entity instead.

Answer to your question: You need to expose the custom table to Views, by telling Views that it exists and what type of data there is in it. The canonical way of doing that is with hook_views_data, although the Data module claims to be able to do this automatically.

Once you have the data in Views, you create a View based on "User", and add a "Filter" to remove all users in the "Payed" table.