Yes I agree with AcheivingGrace it really depends on the antibiotic you are taking.
Some antibiotics just bind with food and get sucked right through your digestive tract. Others bind with metals like calcium or magnesium.
Here is my experience with antibiotics:
Rifampin - This one in my opinion should to be taken on an empty stomach, and NOT with food. If taken with food it tends to just bind to the food and you get a much reduced absorption of the antibiotic. My experience is I only get the really orange pee if I take it on a completely empty stomach and don't eat food for 1 hour after. This one is also easier on the stomach if you take it on an empty stomach.
minocycline - Best taken without food. This one is pretty easy on the digestive tract as well compared to many others. It dissolves pretty fast in the digestive tract too. But some say it doesn't really matter so much with this antibiotic. It dissolves pretty well into the tissues and is absorbed well.
Doxycycline/tetracycline - I have no experience taking these 2, but my guess is that because the dosing is higher, you might want to take with food to cushion the antibiotic.
ceftin/amoxicillin - for me they give nausea if taken without food, so I took these with food and was able to tolerate them better
biaxin - for me I took with food as the dosing is pretty big.
Septra DS - Taken with food... AND this one requires lots of water to flush it through your system after!
Plaquenil - With food and water.
fluoroquinolones - Empty stomach is better. But not to be taken with magnesium.
tinidazole - taken with food is likely better.
So generally it is better to take an antibiotic on an empty stomach... however for some you might not be able to tolerate it so well. If you can't tolerate it, then it is good to take with food. Keep in mind when taking with food it pulls the antibiotic deeper into the intestines killing more microflora, causing more yeast, etc, and the absorption of the antibiotic won't be as good.