If you've been listening to Mr. Silverman, Cerberus is now an "anti-alien" organization. Apparently, they're no longer pro-human. That's why they're trying to stop you from allying and strengthening the aliens. There's our big mystery.
And, in typical Cerberus fashion, they're expressing their anti-alien views by trying to kill the only human who can save the Earth.
It might not make a lot of sense, but only for those who don't know Cerberus well. Here, let me explain.
Fun facts about Cerberus:
1. Throughout both games, they have never hurt an alien.
2. They have, however, slaughtered humans in scores, particularly
their own personnel.
They're all about sacrifice. And the closer the victim to the Cerberus agent in charge, the better. Blood brothers and adopted daughters are preferable. Humanity's best trained soldiers are acceptable. Most brilliant human scientists are tolerable. If nothing else, it has to be a human. They don't experiment on aliens. They don't even care about them.
So, considering that Shepard is both a former Cerberus associate and human, it is logical that they would try to kill him. He's like a never-ending reserve. Shepard can take a lot of punishment.
The problem with Cerberus is that the writers never made up their minds if they wanted an "extremist" organization or a "mad scientists" one. As a result, Cerberus is known as extremists (which is supposed to make them dangerous for aliens), but they act like scientists dealing with highly volatile tech and guided by the deadline rather than ethics (which makes them dangerous for the humans unfortunate enough to take part in their experiments - both the scientists and the subjects are equally endangered).
So, if you want to kill aliens? Don't join Cerberus. You won't be getting what you want. Join the Reds, instead.
But if you want to die in the most gruesome and unexpected fashion? If you want to kill humans in the ways you've never thought possible? If you want to see horrors the likes of which you've never even imagined, and fall prey to them? If you want your last emotions before your death to be shock, confusion, and surprise?
Join Cerberus. Your death will benefit the future of humanity. Your sacrifice will not be in vain.