Worse than that Becca.
Reliance on antibiotics has created the situation where resistant bugs such as MRSA can thrive, and made flora such as Clostridium Difficile the largest "in care" killer in the Western world, according to World Health Organisation. The effect on fungal conditions is at least neutral and harmful, as you state, by your body's natural defences being compromised.
It has got to the stage where at present, NHS trusts are being classed as in breach of regulation (HSCA2008) for sloppy antimicrobial prescribing and from 2012, GPs will be scrutinised too. Sadly, patients have a culture going back many years that antibiotics are the answer to everything, but as Darwin et al demonstrate, the evolutionary playing field alters in size & shape too.
Thrush is an excellent example. Some GPs are still using antibiotics through ignorance and tradition, despite them not working. When challenged, some have actually said it is the government's fault as they need to see x patients per hour and it is easier to give them what they want than to explain what would be better. I had problems believing that myself till I heard it with my own ears at a conference the other year...
Anyway, back on subject fully... Having just looked up a study or two out of interest, (Cochran search,) in answer to the question, Activa yoghurt good for yer guts? The answer appears to be slightly above placebo. In other words, enough for the manufacturers to be able to sell it as being beneficial, and not beneficial in reality. But as they say, mind over matter.