<a href=showthread.php?s=&postid=14190915#post14190915 target=_blank>Originally posted</a> by OwenInAZ
While this is a little broad, it points more or less in the right direction.
Think of each antibiotic as targeting a specific cellular function. For example, Erythromycin binds to the bacterial ribosome and prevents protein production, regardless of species. The difference in sensitivity lies in the antibiotic's ability to penetrate through the envelope and into the cytosol of the bacterium. I'm not convinced the structure of the cell wall itself has much to do with resistance, since on a molecular scale it has huge gaps to allow proteins to pass through. The discerning factor is, IMO, going to be the composition of the cell membrane, and the presence/abscence of any efflux machinery capable of pumping the antibiotic back out. That's not the thrust of your question though, it seems to me.
The very health of a reef tank, much like the health of a human body, depends entirely on the health of its microbial population. A broad spectrum antibiotic is likely to kill off more than just what we don't want, i.e. cyano. A better solution to that sort of problem is to attack the conditions which allowed it to thrive in the first place -- excess nutrients, insufficient flow, poor lighting, etc.