Okay, I've got to ask...do you guys think Flight Sim does anything at all for a person's quest for a pilot's license? I've logged a lot of hours on mine, but I'm worried that instead of helping me learn, it's teaching me bad habits that will be hard to unlearn (turns without any rudder, for instance). What's your opinion?
I can tell you what I've heard from many an instructor, though I am not yet a CFI myself. Almost universally, they say that MSFS people tend to know the procedures for certain things, but are very bad about not using the rudder, as you have already noted. That seems to be a tough thing to correct in many, so the best thing you can do for yourself to assist with unlearning that bad habit is to do the following;
1) Turn OFF Auto-Coordination
2) Get yourself a set of rudder pedals for use with MSFS
3) Turn on real-world weather and let MSFS grab the current conditions to help with unpredictability. Turn ON weather updating at say 10 or 15 minute intervals to provide an even more realistic effect.
4) Turn ON Crash Detection
5) Set the other realizim factors to their maximum
6) Use the kind of aircraft you will be training in and get to know it inside and out
7) Use the Virtual Cockpit mode exclusively to provide the maximum realizm. You won't have a "spot", or "tower" vantage point in the real bird, and the default cockpit view is a little restrictive

Above all, remember that while MSFS is a good "procedural trainer", don't count on it as a substitute for really listening and paying close attention to what your CFI tells you.
Remember too that the CFI is your partner in training, and MSFS can be a tool in your training, but it is secondary, if not tertiary, to your CFI and actual texts and flight experience.
MSFS can not faithfully replicate the sensations of g-forces, turbulence, or even the control feel when taxiing, or other stages. Preflight is something completely ignored by MSFS, and usually most people skip right past the taxi operations, and radio work as MSFS makes that all too easy to ignore.
Having said all that, I will also say that I use MSFS for VFR navigation practice with ADF, VOR, and GPS, and practice with various kinds of instrument approaches (something you won't have to worry about until you go for your Instrument rating add-on). Another thing that it does simulate well is the operational aspects of the radio stack, and the KAP-140 auto-pilot for the Cessna 172. This should not be ignored, as most people do not get adequate practice with learning how to PROPERLY utilize the Auto-Pilot and it can lead to accidents if you are not familiar with how to engage, disengage, and set it up. You may even want to search for the Bendix/King owners manual on the Internet for the KAP-140 (just use a Google search), and review it thoroughly. It will enlighten you as to what all the various features are of the NAV, COM, and XPDR, and AP units are, and how to safely use them.
Just my $0.02. Let me know if you need more info than this.