Keep in mind there are only so many rule changes you can make before the game you are playing only resembles that which the developer created.
These are rules created by people who either do not understand the rules, feel they aren't clear enough or are contradictory. This can be the fault of the writers but sometimes it's just a matter of personal interpretation.
These are written by people with the intention of simply clearing up a confusion in the rules. Sometimes this will be by those of authority such as a gaming store, other times by a consensus of people in a circle of friends.
They're not always correct and official errata / FAQs should be checked and devs emailed before making up your own rules. Be sure to write down your errata so you don't get in rule arguments in the middle of a game.
Some house rules are created because a gaming circle wants to try adding a fun flare to their games. They might be different from game to game and sometimes might not be used at all. Usually you'll see these in the gaming circles of friends since stores have to stick close to the rulebooks in order to create an environment where anyone can walk in and play without surprises.
This could be a random minefield that'll kill either side, a small piece of terrain armies get as a free heavy support choice, mission objectives,
This is where I finally get to use the buzz word of the day - Comp. Compity comp comp compy comp... ahem.
Including, but not limited to Comp, there are entire system changes that gaming stores and tournament organizers (admittedly propped up by many adoring fans) all across the world have created because they believe they can do Warhammer better than Games Workshop. (this can apply to any other system, but I'll continue with GW since it's what I know) When errata starts becoming pages long, you've now entered the area where you're not quite playing the game you purchased anymore.
Games Workshop has been doing their job 5 days a week since the 80's. While we may not always agree with them, they know a thing or two about what they're doing. I'll also point out that unlike some other game systems, GW seems to be trying to just tweak and revise their rules every version to make things better which has the advantage of ending up with clearer and more concise rules, rather than giant changes with potential to be completely different and/or broken. (Anyone who's played DnD from 2nd, 3rd, 3.5 to 4th knows what I'm talking about... at least Tyranids don't have to calculate ThAC0 - wait, do Dark Eldar get Feats now?)
Sometimes it's not actually about balance so much as making things [what they perceive as] fair, knocking down the currently popular or spammed strategies, limiting the amount of vehicles/walkers/dreadnoughts or how many elite/fast/heavy options can be taken (see: all the good / fun units) and/or trying to remove random factors from the game.That's right, people want to take a varying objective, differently terrained strategy dice game populated by _very_ different armies and change it so that people of different skill levels in paid tournaments are on an even playing field as defined by the current local scene.
Personally I think these people would be better off placing their minis on a checkerboard - monstrous creatures can be kings. At this point, they might as well take your previous tournament placings into consideration and add/subtract points from your army size as a handicap or hire those companies that make sure school work isn't plagiarized to weed out net-lists. (My apologies if someone reads this and it's used)
Either play for fun or play to compete. Don't nerf tournaments into Diet Warhammer because you can't stomach a little competition. Lrn2Play. Is this a Win At All Costs attitude? No - I don't play tournaments because I'm a casual player. I play for fun, not competition and I wouldn't want someone to rewrite the rulebook to play in a tournament where everyone's armies resembled each others.
(This actually makes me wonder if the whole Comp thing is in place to avoid the stress of competing - because no matter what, you're still competing and people who stress over it are still going to stress)
Sometimes human nature just rears it's ugly head. Often these will be made by people of power like a gaming store or the loudest talker in your gaming group that nobody wants to disagree with. If you think some rules are junk, say so. Be polite, stay calm and make your point. Talking louder doesn't actually help AND NEITHER DOES TYPING IN ALL CAPS.
A while ago an example came up where a gaming store (I believe it was actually a Games Workshop) allowed anyone who bought terrain at the store to place it after both sides had setup their units. Obviously this can seriously change a game. Motive? Money. Other times this might fall into one of the above categories but be obviously unbalanced and in someone's specific favour. If you want to try other rules, go for it - but if they appear unbalanced, you have to say so and not allow their use to continue if you can't balance them in a reasonable amount of time.
Believe it or not, some people don't care if they win fairly, as long as they're winning - luckily I haven't had to deal with this personally, but Internet has plenty of examples of this. Sometimes it's cases of people flat out cheating. There seems to be the opinion held by some (and admitted on forums and such) that "If my opponent doesn't know I'm not quite following the rules, then I can do what I want and it's their own fault."