They're not similar at all. FoCS is mostly about introductory programming and data structures (with a tiny bit about automata). Sipser's book is about computation and complexity - it's comparable to Hopcroft and Ullman's Intro to automata theory, languages, and computation, for which Ullman recommends FoCS or equivalent as a prerequisite.
Coincidentally I just signed up for Ullman's Automata course at Coursera. The description makes it seem pretty basic but I'm interested to see what he does with it.
