The dirty secret is there are practically no decent, affordable "authentic" Swiss restaurants left in the center of Zurich, if by that you mean cheese, meat and potatoes-style dishes.
Here's are two within a stone's throw of each other off Paradeplatz; Zeughauskeller is very popular with tourists, but I never cease to be amazed how many of my work contacts--native Zurich--love it as well:
There are also a couple in Niederdorf that I have heard are quite good, like Bluetige Duume and Weisser Wind, but I haven't tried them.
These are mostly Swiss-German style places - I have yet to find somewhere which serves decent filet de perche or papet vaudoise, but then again it's not too far to the French part...
Dito here, Alpenrose is very good. The only "problem" with Alpenrose is that "ignoramuses" who believe that swiss food is melted cheese, period, will tend to claim that the food there is not actually swiss...
If you're looking for cowbells and fondue, stick to the touristy places. Should you want a good restaurant selling swiss sourced food, you're spoiled for choice, but beware most are mid range+ in price.