The thing is, the extent of the NCR's 'evil' is overtaxation and, if the Khans are still around, them gradually being driven out of the Mojave; Caesar's evils are far worse in terms of slavery and generally the brutal culture he imposes. Sure, it's all about perspective, but you have to question the morality and reasoning of someone who considers Caesar's legion as the better option for the wasteland. The way I see it, it's not really a matter of picking the side which is good, but picking the lesser evil, and Caesar's Legion is never the lesser evil purely going by the end slides.
I think the faction the users here holds near and dear to them speaks about who they are as a person ideologically speaking.
NCR fans see the NCR as good are likely supporting NCR because they believe in the 'American Ideal', IE Democracy at all costs, seeing overtaxation and people being forced off their lands because NCR claims it as their land by force as things all for the greater good.
Legion fans see the Legion's brutality and 'evil' behaviour as justified because the Legion, like it or not, their means do justify the ends. If Caesar wins in the Mojave, as brutal and savage as it is, he has an established society of law and order. Crucification is for disobedience and failures, as well as punishment for various crimes, or it's used as a scare tactic for enemies. For the people who support the Legion, the issue isnt that difficult, compliance in return for safety and security, which really isnt all that different from Elijah's plan, although I fail to see how killing people with a toxic cloud is productive in building a nation. Anywho, point in short. NCR rules with the threat of laws and jail, Legion rules with threat of pain as punishment or death. It's a harsher system than NCR's, but it works. Steal something in NCR land? A year or two in jail. Steal something in Legion territory? I dont know about you, but the idea of crucification or death scare me ALOT more than jail time.
For House fans, such as myself, the ends justify the means because for starters, what better than an army of robots? They're self sufficient and no lives are lost in war on our side if you have no humans on the ground. A machine is replacable, a unique human life is not. Ensuring a technocratic and progressive society is important because it allows advancement on a scale of Pre-War measures. For us, the idea is most likely 'this technology could do the Wasteland alot more good than 'governments' or 'barbarians'. We also recognize sacrifices must be made for the greater good. Kill the Brotherhood? Alright, they werent doing anything but wasting space. Convince the Kings to start a war with NCR? Alright, it helps keep NCR influence out of Vegas. For the House fan, pragmatic choices for the greater future are important. It doesnt matter if the choice is considered evil in the now if five years down the road it's built a brighter and stable society. So progress is important over individual people. Some may say I've not made any negative point about Hous supporters, but I have, it's just a subjective idea. If you think people are important over progress you may have a lot of doubt in your choices you'd have to make sometimes. We may not be devoid of emotion, but sacrificing the lives of a handful to save hundreds if not thousands is the pragmatic choice.
Indie fans I can't rationalize because there is no real 'general' touch. Each would support it for their own purposes, which is a myriad of attitudes I dont want to try and name and spend all day on.
Point is, supporting one faction that YOU (You being the character you made using the choices you yourself would make, not your RP character) make isnt about good and evil, it's about which faction is a mirror into who you are deep down.