Haha, I remember when I first read the books, I was sort of rooting for both. (That is, I wanted Artemis to outwit the fairies and get the gold, but I didn't want anyone to get killed. So I guess I got what I wanted. XD)
I think part of whether you think of Artemis as a villain or not comes from how you would define a villain. For me, I still think Artemis was the real villain of the story for several reasons. (Even if in the end he did prove to have some redeeming qualities.) He did a lot of cold things—for instance, at the beginning of the book, we have no reason to believe that he wouldn't have let the sprite die if she had refused to relinquish her copy of the Book. However, he did honor his agreement (if he did seem to take a bit of a sadistic pleasure in the idea of her pain at expunging the alcohol), which made him less dislikable as a villain than some of the later villains, such as Jon Spiro or the Russian Mafia from TAI. (Who did break agreements as a matter of course.) He also set the bomb on the oil tanker, which could have very easily killed Root or whoever the officer sent after the tracker, though Root did manage to get off in time. Artemis may not have intended to kill the fairy, but he was more than willing to risk it.
We also have to remember that it was Artemis who initiated contact with the People, knowing full well that his scheme might potentially kick off a war. And the stated goal of all these ruthless things that he does is to obtain gold for the purpose of restoring the Fowl family glory. (In TTP, Artemis age 10 was looking for money to fund the search for his father, but in book one, he decides to give up on the search and accept his father was gone, in order to succeed in his plans, even if he seems to regret this later.) Artemis does have stabs of conscience periodically over the course of his scheme, but in the end, even after his hostage stepped in and had mercy on his servant by saving his life, he still will not relinquish the gold.
Artemis does have moments of conscience throughout the book, and does honor his agreements, but I think those things show his potential to become something better, rather than excuse him from the title of true villain.
Of course, one of the things I love about the books is that the People aren't perfect either. You have true heroes like Root, Holly, and Foaly, who really are concerned about preserving life and are willing to risk their own lives to save that of their friends and comrades, and to protect their entire race, and yet you also have political shenanigans from fairies like Cudgeon, and a ruthlessness from the Council when it comes to protecting taxpayer gold.
Plus, even the heroes of the story, are shown to have their own biases. As you said, they have a superiority complex, and look down on humans as being both mentally and morally inferior. (Holly herself has an interesting thought near the beginning of the book, where she thinks to herself that she can't 'kill the troll under any circumstances. Not to save humans.' Holly seems to have a heroic streak she can't put down, and always jumps in to save lives whether they be human or fairy, but it seems clear that her culture tells her the life of a troll [a magical creature, but essentially an animal] is worth more than that of a mud person, or even a roomful of mud people. The People's prejudice against humans and lingering bitterness over being driven underground seems to be a theme that lingers throughout the books.
I still think, in essence, in book one Artemis is 'the bad guy' and the fairies are 'the good guys' (again, Artemis initiated the contact in order to steal their gold, and essentially blackmailed them by threatening to expose their existence to the world, which would have likely gotten them all slaughtered, while the People, though they may have been ruthless, had to act and do what was necessary to protect themselves from the attack), but I think one thing that makes the books so interesting is that there are those shades of gray in between. Artemis isn't totally bad, and the fairies aren't totally good.
Oh, one last note—it's true that when Artemis Fowl Senior's ship went down, Artemis had to fire off a lot of the staff and they were really struggling to make the funds they needed. However, in book one I think it's stated (or at least implied) that Artemis had, by that time, rebuilt much of the Fowl empire, and his goal in stealing from the fairies was to return the Fowls back to billionaire status. (The Fowls were no longer struggling financially, but they had fallen from their former position of glory and prestige in the world, and Artemis's goal was to win it back.)
Anyway, that's what I think. But maybe I just like thinking of Artemis as a villain. XD (In the early books, at least.)
“After all, absolutely no one can help but suspect a criminal, liar, and manipulator of committing crimes, lying, and manipulating. And of course, no one is more aware of that simple fact than Artemis Fowl.”
Opal sets into motion her most diabolical scheme yet, to frame Artemis and turn his closest friends against him. Only this time she has a new calculating partner who knows Artemis better than he knows himself. [An Artemis Fowl fanfiction, set after The Atlantic Complex.] https://www.fanfiction.net/s/8336552/1/Noble-Heart
...Shameless self-advertising, guys! C;
(And if you're really bored: http://axxonu.deviantart.com/gallery/28912232/Artemis-Fowl
AF fanart. ;J)