I've been exploring a bit and having a great time doing so, however...
I have a great relationship with the Liberty Navy, no problems there. But recently I tried going through a jump hole in the Texas system and as I arrived at the other end I was instantly destroyed. This was a rather large problem as I hadn't saved in a while and the autosave had set to when I came out of the jump hole. I began to realise the people attacking me were the Liberty Navy GUARD, and I had no idea why. After millions of failed escape attempts I eventually managed to escape back through the jump hole.
But why? Why is my rep with the Navy Guard so crap and my rep with the Navy really good?
Think of the Guard as of the sentry of a military base, and of the Guard systems as of the military base itself. Sure, you may be friendly to the soldiers walking around town, but you can't just enter the base, right? You would need to obtain a special permission. That is, to get your faction-guard reputation to white. It is connected to the regular faction reputation, and you can fix it by doing missions for the (in this case) Liberty Navy
I think it takes between 5 and 10 missions to get them neutral. And you can find high ranking missions, but I find the easiest to be station missions from the Battleship in Texas against Xeno or Rogues. Much quicker to shoot things that don't move.
This is something I noticed, and I provide you the same answer I was given:
'They're a Guard Faction. They start hostile.'
Which means exactly that. You need to do a metric frakload of missions for their friendly factions to make them friendly enough to not blow you up. Worth it when you're cruising around Alaska without getting blown to bits by Order and Nomads though! Word of advice, never go in Alaska unless it's just you or you're in a group. I think you can be fired on in-RP just for being there, regardless of your faction status.