How about congress's right to establish rules regarding the elections of its members ?
If they can make it illegal to criticize the candidate in a commercial ad, why not just make it illegal not to vote for the candidate? Who needs pesky election anyway?
Your interpretation of Article I is quite broad. You should read it. It mentions the "time, place and manner" of elections." I don't see that as allowing banning political speech via commercial ads. Furthermore, the main power to regulate elections is given to the state legislatures-- not Congress.