I have no idea how this guy is going to execute the reboot and frankly have no enthusiasm as to whether I want to watch anymore X Files, but...
...do you understand the original series was written with the social and political context of the 90s in mind? Distrust towards the state, jolts of liberal economy, xenophobia, workplace alienation - basically the whole political gamut of American consciousness had been rotating themes throughout the show. For example- and I chose to mention this for no other reason than you've done so rather teasingly- I remember white supremacist characters popping up on the old series semi-regularly (one of my most memorable episodes wherein Brian Cranston plays a guy with bouts of excruciating head pain happens to be a redneck and a bigot).
So why should the idea of the same approach being practiced in a more contemporary setting become such an execrable notion all of a sudden? You guys seem to have detatched from the reality that used to be unto us 2 or 3 decades ago, leading to the misapprehension that television, generally postmodern art did not use to play off politics. It might have proliferated in recent times but these things have always been there.
If you don't want to see politics in a cop show, you'll be left with Twin Peaks and nothing else.