Avoiding "Usage of a direct database call is discouraged"

WordPress-Coding-Standards reports that "Usage of a direct database call is discouraged."

It's complaining about my usage of $wpdb->insert() in a plugin. Is this not recommended? What is the correct way to insert data into a plugin's database table?

Or can I just ignore this error? In which case, is there some system to mark it as reviewed and not to be flagged again?