Famara Diedhiou and Matt Taylor scored in the second half to lead the Robins to an impressive win against the Premier League opponents at Ashton Gate.
Following the game, Hughes said: "We were poor and they played very well".
"It is important that we progress in the competition, so we want to have a good run in it this season if we can".
"I am very disappointed because this is a competition we wanted to do well in".
Defender Glen Johnson, midfielder Charlie Adam and striker Peter Crouch are all in contention for starts.
Ryan Shawcross and Geoff Cameron are both expected to miss out through injury.
Tickets for the game remain on general sale, with prices starting at just £13 for adults and £6 for under-19s.