They just tend to be seen as not as good. They're generally easiser to get into as offers are lower, teaching standards are lower, graduate employment is lower etc. I'm not saying all ex-polys are bad, but look at a league table and it's just a general trend. You have to bear in mind, there are other new universities such as Warwick that are actually really good, so it's not necesarilly to do with the fact that they've not been round for a hundred years.
Either way, it doesn't necessarily mean all ex-polys are bad, and attending an ex-poly makes you dumb, they can actually be pretty decent for more vocational courses. It's mostly just a case of academic snobbery (which is rife of TSR).