What exactly do you mean by a "flatfile" database backup? Are you referring to just copying the .MDF and .LDF files to a different location?
If so, then the biggest con for that method is that you will only have a reliable backup if SQL Server is not running, or the database has been detached before you begin to copy the file. Additionally, the size of your backup will be the size of the .MDF(s) + .LDF, which could be huge. A native online backup (without compression) will be the size of the actual data in the .MDF, and a small portion of the transaction log.
A native online backup (or one using a third party backup tool) is always a better solution than just copying the files.