In the connection Properties tab for your database connection under the SQL Commander category, you can enable Strip Comments when Executing among other settings. You may also do this for all your connections of a specific type in Tools->Tool Properties and the Database tab. Select the database type and then do necessary changes under the SQL Commander category.
Some databases handles comments just fine while others don't. The strip comments feature in DbVisualizer is available to handle these cases.
Ah, interesting, thanks. I appreciate the swift response.