The argument for the joke is obviously that since pro and con are opposite prefixes so therefore progress and congress would be opposite because pro and con are. This is not taking into thought the actual definition of either word, rather the prefixes. It is meant to be a joke and the wording does make sense.
No, even though congress has been messing up a lot lately, I don't think you can call them the opposite of progress. Congress has passed bills that made progress, but the bills they don't pass are the ones that get more attention, negativity always gets more attention than positivite acts.
While it would be an obvious joke to say that the opposite of progress is congress due to the lack of popularity among out current government, it is just not true. Progress by definition means to move forward towards a destination. Congress on the other hand means the national legislative body of a country. Therefore by definition they are not opposites, but just different things entirely.