Flora is basically any plant or bacteria. It is interesting that a large minority of the biologics in the intestines are actually fungi, which used to be classified as flora but have been reclassified as heterotrophs. Since the term intestinal flora has been used for so long and most of the biologics living in our intestines are bacteria (most of which die when exposed to air, interestingly enough) the name has stuck and most likely will never be changed even though it is not quite correct.
Another interesting aside is that the bacteria that CAN live when exposed to air are in an oxygen poor environment, they cause fermentation instead of acting how normal cells do (use oxygen to create energy). This fermentation leads to gas buildup in the intestines which, obviously is expressed as nasty farts.
But to directly answer the OP, I have found no information that says any injectable steroids cause damage to the intestinal flora. I have found anectodal (non-tested or proven, but quite possibly true anyway) evidence that shows taking steroid pills causes damage due to the other items contained in the pills. Basically what Mrrippedzilla said. As chicago712 said, taking probiotics can only help...even if there is no harm being done. There are many side effects and diseases that can happen when the good bacteria is killed off in the body and some of the bad bacteria start to take over (the most common side effect is horrible gas), so if you are worried, just pop some probiotics and let the worry vanish.
It is a great question and gave me a topic to research today. I love research, it makes me happy...yes, I am strange that way.