Remember... the definition of "hero" is someone who uses their strength for the sake of others.
Now, while Varis may be a terrible villain to the Domans and Eorzeans - bringing his country's might to bear against them based on speculative reasoning - to the Garleans he's a great hero, using his military prowess to protect them from the savages who would do them and the planet harm. (Of course, if the average Garlean citizen would get out there and see the provinces and other countries for themselves, they could easily hold a different opinion from what the Imperial propaganda machine spews. All of the "good" Garlean characters we've met have done exactly that.) He is, technically, using his strength (military prowess, tactical ability) for the sake of others... his own people, albeit at the expense of the rest of the world. ("cuz they were horrifically persecuted!" - Irrelevant.)
What makes Varis so dangerous is, like LineageRazor said, his unwavering, arrogant belief that he and only he knows what's best and right - that he and only he can save the planet. Since what he does is for the survival of the planet, anything can be justified. It's fair to say this makes him similar in that regard to Thordan, who much like DBS' Zamasu was said to "[believe] only in himself" verbatim.
The thing is... a lot of people disagree, both on whether the means Varis is willing to use are acceptable and whether the world he wants to create is ideal. Given that his goals involve killing and/or effectively enslaving everyone who isn't Garlean... naturally, just about everyone else in the world is going to be against him. Garlemald's successes are, in no small part, a consequence of the rest of the world being unprepared for just how powerful its war machine is and not standing together against it. Now that's happening, and the tide is being turned.
Anyway, I digress. Varis uses his strength for his people, which makes him a hero to them... while that strength brings nothing but death and ruin to the rest of the world, which makes him a terrible villain elsewhere. Even if he does (or commands) evil things, they're for the benefit of his people... which makes him not objectively evil, and that is why war is so tragic. (The Eorzeans and Othardians, on the other hand, have never done or condoned any morally questionable acts against Garlemald, and have only ever fought to defend their homes or reclaim seized territory from the Empire... so for most intents and purposes they are in the right, and acting against the Empire in the capacity they do can't really be construed as "morally grey." [X thing Y Eorzean nation / Doma did Z years ago] is contextually irrelevant - Garlemald isn't attacking Eorzea because of the War of the Sisters, for instance. This is a red herring - a non sequitur, to be specific.)
Since it's... somewhat relevant, let's look at Sylvanas' motivations for the War of the Thorns in WoW. With the advent of Azerite (analagous to mako energy, for those not in the know) she feared that the Alliance would develop Azerite superweapons as well, which combined with her belief that the bad blood between the Horde and Alliance would inevitably spark a war, would lead to mutually assured destruction. Therefore, attacking and forcing peace on the Horde's terms, while very questionable, was preferable to that mutually assured destruction.
Now, there are a number of problems with Sylvanas' strategy that would have rendered it ineffective even if her plan had gone off without a hitch (killing Malfurion would have just martyred him a la Varian, and supplemental material reveals that Greymane would not have abandoned and consequently splintered the Alliance like she anticipated) and I in no way at all would ever condone starting a war based on speculative reasoning (much like with Garlemald), Sylvanas' logic does have... some merit to it. The conflict really was morally grey... until she killed roughly a thousand civilians due to Saurfang causing a setback, deployed chemical weapons against friend and foe alike, desecrated the remains of those friends and foes, used what was more or less a false surrender to try and kill the Alliance leaders, and rendered a large swathe of land uninhabitable.
Are the things she does evil? Undeniably. Is the Alliance in the wrong to fight back? Not one bit. But... as long as it's to prevent mutually assured destruction (or less charitably ensure the Horde's prosperity), Sylvanas' actions cannot be condemned as wholly evil. She's meant to be seen as "pragmatically ruthless," and while I personally condemn her methods and ends that is what she objectively is... not unlike Varis. (A world where everyone can at least coexist in peace and freedom is far more ideal to me than the world either of them want to create, so naturally I sit in opposition to both.)
Of course, both hinge on their stated intentions being honest. Sylvanas seems... rather shady, but Varis seems to be honest in his intentions... though I again question what he would do if forced to choose between his people and his ideals. That would be the true test of character for him as a ruler.
I've rambled long enough.