I have a 13 year old gelding that was on the bottom of the pecking order for most of his life. He is docile most of the time, but he exhibits strong food agression even though he is in a private stall and being fed well.
Food aggression can be a difficult thing to deal with in horses. It is often caused by insecurity. We often see it with neglected horses who were not regularly fed: once they start getting grain they don't want to let anyone near their food. We also see it in horses who are group fed and have to fight other horses for their food. Since you say your horse is the bottom of the pecking order, I would say his issues come from insecurity and probably from having to fight to get his food earlier in life.
I haven't found a 100% successful way to cure food aggression. For neglected horses, sometimes once they are on a regular feeding program, over time their food aggression with slowly decrease and eventually go away. For horses who are fed in a group situation, separating them from the group to feed them may help lessen their food aggression.
You don't mention how long your horse has been stalled for feeding. If you've only recently begun that, then I would give it time. Some horses, though, never get over the issues that create food aggression.
With any food-aggressive horse, you need to give him a safe place to eat: a stall of his own, preferably with no one next to him. Leave him alone to eat - don't clean his stall, groom him, hang out with him, etc. while he's eating. If he has a tendency to bite or kick at you when feeding, set his stall up so you can dump his feed into the bucket without entering the stall.
Good luck - and I hope some time in a safe environment will help your horse become less food aggressive.