How to secure your FOB?

I can tell you what is the most effective strategy (at least at low levels) from invading a few times myself.

1. Fill your security staff with all of your worst Combat soldiers (Ds and Es). This will ensure none of your good combatants are stolen, and it really doesn't seem to make that much of a difference for guard duty.
2. If you have extra GMP, install decoys. Decoys can cause an invader to screw up and attract guards if they're not paying close enough attention, but the "real" (more reliable) benefit is that the enemy can't know your true guard count because adding decoys inflates the number of guards listed on your platform.
3. Once you inevitably develop it to the point that it's actually worth defending, security devices aren't exorbitantly expensive and make the invader's job much harder. It's easy to pay attention to guards and decoys. It's hard to pay attention to guards, decoys, IR gates, drones, mines... the margin for error becomes much smaller.
4. Hold off building your Base Development Platform. When people invade it, it's basically just a giant warehouse filled with all of your resource containers, so you give them the opportunity to steal them from you.
5. If you do have to build a new platform, stack decks on it. Decks make your security exponentially tighter; when someone invades your platform, they start on the outermost deck. In other words, if you have 4 decks, an invader will always have to go through 4 entire decks to get to the goal point. Not to mention, your guard capacity is limited by your decks, so you have roughly quadruple the guards of a guy with 1 deck.

And, GP89 is correct when he says that it's incredibly easy for someone to make a mistake and give you an instant win, even on minimum security platforms... my last invasion ended in a suicide after I accidentally pressed the stance button while climbing on a pipe. I was spotted and panicked; I hit the stance button because I thought I would slide down like on ladders, but I fell five stories onto the deck and cratered. Easy money for the defender.

Invasions are tough relative to normal missions. There's just so many angles that guards can spot you from with all the catwalks, and pipes are the absolute worst climbing device -- they're like slow ladders that you can't safely exit quickly and leave you completely helpless. You have the advantage as a defender. Also, keep in mind that in conventional missions, you can escape much more easily from sticky situations due to the open nature of the terrain. Decks are constrained to quite limited areas, with some underhanging catwalks to hide in. Hiding places are few and far between, so you're virtually always either dodging a guard or taking one out, or both. This game isn't quite like Dark Souls so you don't need to worry as much if you get invaded.

P.S.: The invader also loses heroism instantly upon killing your soldiers. I tried the "panther" approach (just take silenced lethal weapons, sneak as fast as possible and shoot anyone that spots you) and I stopped as soon as I saw that happen.