First of all, yes, always give probiotics when they are given meds, as it absolutely does make a difference. The meds are harsh on their stomachs and the probiotics settle them and keep their appetites up, and most antibiotics kill off the normal flora in their gastrointestinal tracts, and the probiotics replace them. Without probiotics the meds can kill off the normal bacteria found in the gastrointestinal tract, which often results in a secondary yeast infection in their gastrointestinal tracts because the normal bacteria is no longer present to keep the yeast at bay.
Baytril (enrofloxacin) is a Broad-spectrum antibiotic, but you need to figure out what the third bacteria they detected is, and what the count was, because if it was Coccidia, yes, it is normally present in low counts and does not need to be treated, but in moderate to high counts it is too prevalent and does need to be treated... However, Baytril will not treat coccidia, coccidia is a Protozoan infection and requires an Antiprotozoan medication, like Toltrazuril (Ponazuril), not Baytril. Proteus and ecoli infections are common bacterial infections, should clear pretty quickly, but again if it was coccidia that was also cultured and diagnosed, you need to not only confirm but also find out the load or count level...
Could it have been Klebsiella?