As a new DM with a group of new players it would be best to completely ignore this section. Learn the official rules and become familiar with them. Rely on the book to dictate rules. Let the books, in most cases, be the final arbiter.

However, every version of D&D has had rules that I didn't agree with. Most DMs make small changes here and there. Others make sweeping changes in order to match the game to their vision. Some make so many changes that the game is no longer recognizable as D&D to an outsider.

That's fine. Your game is yours to run as you see fit. To be fair to your players, you should document any changes that you make though. With previous versions, I have even printed my own PHBs for players to use containing my full set of house rules.

Pitfalls

Be very careful when making changes to the rules. Everything is tightly wound to everything else. It would be very easy to unbalance the game by changing a rule that has unforeseen side effects.

One trick to testing a new rule is to try to break it. Imagine yourself as each class of character. Look through their powers and feats. Does this new rule increase the effectiveness of any of their abilities. How could you use that to your advantage?

If you have a player who is skilled at looking at rules from an unusual perspective, ask him to try to break it.

The worst part about house rules is that most utilities have no way for you to incorporate the new rules. Even something minor could affect one of the tables on the DM Screen. Then you have to tape a sticky over it with the new info which just looks cheesy. More serious would be a change that affected your players' ability to use the D&DInsider utility to level their characters. That means losing a pretty cool utility.

On The Other Hand

I intend to write many articles on this topic as I have already decided on a number of rules that I intend to rewrite and some are so basic that they require lots of other changes to support them. :)