We are building a (non-native web app) that looks and behaves like a native iPhone app (using jQuery Mobile). Now the client wants a fixed footer menu which reduced the screen estate. Is a footer menu bad practice?
Depends. In your case, it sounds like this menu is too tall. But something the size of the iPhone's tab bar is beneficial as iPhone users are already used to this method of navigation.
If the menu is too tall, consider having a drop-down (or I guess drop-up in this case) button.