While I've no doubt this question is going to be raised constantly until release, I'd like to offer one dissuasion up front:
Whatever the Reason, 'Shepard knowing too much' is almost certainly not it. Shepard is already outside of TIM's reach, and can communicate/leave dead-man's-drops at any stage. Along with Liara being Shadow Broker, if Shepard wants something to get out... killing him won't stop it.
That said, I reserve skepticism until otherwise proven.
Who, for example, is telling us that Cerberus is after Shepard? Are they even correct, or might this be a false flag? If they are correct, is this a TIM-sanctioned operation or someone else's initiative? How has Cerberus tried to do this? Is assassination even their goal, as opposed to forcing Shepard to keep his head down? How long has this occured?
We can go to the lazy 'TIM has no use for Shepard anymore' or 'Cerberus is indoctrinated' arguments, but with what we have we can just as well provide others.
Cerberus knows why the Reapers want Shepard, and have placed a priority on denying it to them.
In the interim, Shepard 'stuck it to Cerberus' in some unknown action and Cerberus is retaliating.
Or it could be a false flag operation.
Or, my favorite, Cerberus isn't actually trying to kill Shepard per see, but by forcing him to keep his head down they are keeping Shepard out of sight (and alive), with the intent towards driving him to what may well be the safest place in the galaxy for him: an Alliance courtroom. A case of 'we don't think we could actually kill you, but we could cause you to react in the way we want you to.'