Especially after the start of the War on Terror (the Afghan and Iraqi Wars), Huey Freeman would rant about Bush and his cabinet at almost every opportunity, while Michael Caesar cracked jokes about them. It got to the point that this became the favorite hobby of Huey and Caesar.
Bush isn't really mentioned so much in the TV series, although there are two Iraq War veterans named Ed Wuncler III and Gin Rummy, who are also meant to mockingly represent George W. Bush and Donald Rumsfeld respectively.
President Bush later does get mentioned by name in "The Uncle Ruckus Reality Show". While Uncle Ruckus is visiting a black barbershop, the barber is ranting about Bush and the Iraq War to one of his customers. Ruckus, as a card-carrying Republican, then has an argument with the barber.