Depends on the antibiotic. Some at better taken with food because they can upset your stomach. Some work more effectively and are absorbed better when they're taken without food. This must be one of those. They're not bad on your stomach necessarily, although after you've taken them for a few days they can kill out some of the beneficial bacteria in your gut (that doesn't always happen). The pharmacy probably knows that this one works best and gets absorbed better when you take it without food.

One of the things about many foods, like milk and yogurt and cheese, is that they contain micro-organisms (good ones, nothing dangerous in most cases), and so when you take certain antibiotics with those foods, the antibiotic will go to work trying to fight the naturally occurring bacteria in food instead of on your infection. Many of the penicillins are notorious for doing that, which is why they've told you to take your medicine separately.