It's most often used in pro audio because pro audio engineers knows that sound engineers are complete morons that will sometimes connect an XLR output from one amp to the XLR input of another amp. But the easy way to avoid damage is to just add a clamp on the input.
It's used in pro audio to match impedances (in particular with microphones), in DI boxes (to allow otherwise incompatible gear to interact, eg iPod for sound checks, direct boxes for plugging guitars directly into consoles, etc,) and to allow the inevitable long cable runs without significant HF loss and eliminate ground loops. They also block DC, and RF interference. Surely these are not all undesirable features in an audio chain.
It is probably impossible to buy a recording that does not involve listening to transformers used to create it. If you have even one favourite recording, I am going to suggest they chose the audio transformers wisely.
There is very little to dislike about a well-designed and properly implemented audio transformer, sonically. There is much to dislike about poorly designed and improperly implemented transformers sonically. Mostly they are used less today because they tend to be heavy and expensive, not because they inherently sound bad. Far from it, but, like everything, the chosen unit must be appropriate for the task.
Almost every time I heard a "bad" transformer you could trace the essence of the problem to trying to get away with choosing a cheaper example when the design calls for something that actually works under all expected conditions. They are certainly not the ideal answer to every audio problem, but on the other hand I find my life much easier when I don't dismiss well known working solutions out of hand.