Uhm... you can't "allie" with any faction, instead, you can get "friendly" with that faction, wich means that their ships will be tagged as friendly (green) and you can dock on their bases/planets and buy equipment/ships from that faction.

How reach that? Killing their enemies. If you go to the panel where all the factions and their reputation towards you are listed and click in a faction, you will se a short description of the faction and a list of allies/enemies. Killing that faction enemies will make that faction and (in less range) their allies friendlier to you, and of course the attacked faction (and their allies) more hostile to you.
Be cautious: You can't be friendlier of everybody in the vanilla game.

Good luck out there

But one bar in the "friendly barometer" is olways missing...

The way it is. Only time all bars are even red, is in missions during mission game.

Hmmm ... hadn't noticed that. I'll have to check my "hostiles" in the post story line game.