From the source you found:
To a large extent, Colbert's show and the character that he created are based on the O'Reilly Factor, by Bill O'Reilly. Colbert frequently refers to O'Reilly as his mentor and calls him "Papa Bear" in an endearing manner — a nickname with a subtle double-meaning, as Colbert constantly states that he considers bears to be the #1 threat to America today. Colbert makes no secret of his spoofing O'Reilly: upon hearing the news that O'Reilly said he likes The Colbert Report, Stephen declared on-air that "I like you too. In fact, if it wasn't for you, this show wouldn't exist."
So I'm not the only one who thinks the "papa bear" moniker has a double meaning. :rofl: