She doesn't seem poor and lives off with free food and WiFi, right?
Internet searches for Cheesecake Factory waitress salaries range from $27,000-$33000. This may or may not include tips, but tips are shared with the kitchen. As you note, Penny freeloads quite a bit. Her car has had the engine-check light on forever.
Her apartment is not flashy - the elevator hasn't worked in 7 years. The PhDs across the hall are researchers, not professors, so their salaries may be quite average, and Sheldon keeps a roommate because he needs a driver.
Surely there are plenty of waitresses renting average apartments in California.
Additional Info (9/23/13)
On the episode entitled "The Cruciferous Vegetable Amplification," Penny owes Leonard for several takeout dinners plus a month's rent which comes to "a little over $1400."
I found a potential answer to how Penny gets by here which explains a bit about California labour law and factors in the tips she would earn while working at the Cheesecake Factory;
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This is a very old TV sitcom question. In multiple shows the protagonists live in apartments that are way beyond their means. Often, the apartments are huge or luxurious and in neighborhoods (mainly Manhattan) where the rents are astronomical.
Sitcoms are farce, not real life. The producers create spaces that are visually striking and easy to film around from one point of view; the camera never moves.
She lives beyond her means because theproducers want her to.
Notice that the Cheesecake Factory where she works is far more low rent than the restaurant is in real life; because the producers want it that way.