Corporations are simple to vilify. They're a faceless alien entity (despite just being an abstraction of a group of investors and employees who are human, after all). They have no race (although they are usually represented by a white male mouthpiece). Their goal can be easily construed as making a profit at anyone's expense (regardless of what they might in reality be contributing to society).
Look to the Alien Series and Wayland-Yutani, "The Company". It's the template upon which all modern Evil Corporations are based, despite their business model making absolutely no sense.
They spend countless trillions setting up colonies and investing in the future of mankind, are seemingly the driving force behind every major piece of technology in the setting, and yet they are willing to throw it all away for a chance to try and tame an alien species that time and again nearly spells the doom for humanity.
Why do they need this alien? Yeah, it's cool and has some unique abilities and properties that would be useful to the bio-weapons division, but they already dominate all of known space. Who exactly are they going to use these aliens against that the Colonial Marines couldn't crush more easily and cheaply? The Alien is not a WMD, it's an ELE. It's the History Eraser Button. For Christ's sake, don't push it!
LexCorp, TriOptimum, Cyberdyne, InGen, Tyrell Corp, Umbrella, ExoGeni, Microsoft, Massive Dynamic ... the machinations of each threaten the very existence of humanity on a daily basis and yet their stocks never go down, even when they end up nuking some midwestern city to coverup one of their "mistakes".
Does it make any sense? No! Is it still awesome in the context of sci-fi for the heroes to stand against The Man who is willing to kill everyone including Himself to make a buck? Hell yeah! Most of the coolest sci-fi stories couldn't exist without the Shadowy Cabal of Sinister Business Interests driving the plot.
It's like Anwar already said, businessmen are the new aristocrats, who were themselves the new capricious gods who did evil shit because, fuck it, they're EVIL and being evil is fun! Mwwuuhahahaha!