Antibiotics kill all bacteria of the type they are effective against (gram-negative or gram-positive). Antibiotics do not magically decide which are good bacteria and which are bad. This is why you should take probiotics after you've used a systemic antibiotic (as opposed to, say, Bacitracin applied to a wound) -- to repopulate your gut with good bacteria.

Here's an article that explains the difference between gram-positive and gram-negative bacteria

http://info.achs.edu/blog/bid/282924/medical-...e-bacteria