I have also been scammed out of funeral pay in the past (thankfully, never weddings). In two ways:

1 - A job where they WERE stipended, but when I met the substitute organist after taking the job she informed me that she played most of them. She had been there for decades, knew everyone, and there wasn't much I could do.

2 - A job where the priest looked me in the eye and shook my hand, agreeing that weddings and funerals would be on top of the salary we had just negotiated. And then proceeded to take a funeral musician fee from the family, but not pass it on to me (took me a couple months to get wise to this). This was to "help pay my salary" according to him. Very nearly quit over that one, but ultimately I still got wedding stipends and the funeral fiasco alone was not enough to push me out. Things improved later with a different priest.

Both of which to say - even when you think you've negotiated this, there are pitfalls. If it's not in writing and signed by all concerned, well...

But at the same time, wedding and funeral stipends are BY FAR the norm, and I wouldn't blacklist the entire profession because of the backward/ignorant exceptions.

Is unethical treatment the exception, though?

In general, I think so. And often it happens out of ignorance, not malice. Some hole-in-the-wall churches don't realize that it's standard to receive extra stipends for these things, especially if BettySue volunteered for the last 26 years prior to your arrival. Then there are the priests who emphasize the "ministry" aspect of it, so they think that they are achieving a moral good by not nickle-and-dimining parishioners, not realizing that it has a significant effect on your bottom line when supporting a family and paying for a mortgage. And while many of us all have a story to tell, many of us have worked for multiple churches. So if only one of the 6 parishes I've spent any time at has had an issue, it's a statistical minority at least in my dataset. But I've done this for many years at this point, and have encountered lots of different churches, priests, secretaries, etc. It only takes one business manager with a bee in her bonnet (or a pastor for that matter) to upend the apple cart. But that's a "them" issue, and not necessarily indicative of the broader culture. Most places I have ever played (catholic or protestant) have had absolutely no issue whatsoever making sure I was paid. They were usually thrilled I was even there to begin with, since bonafide well-trained organists are increasingly rare.

Interestingly, I'd wager that many of us also have horror stories about other, non-financial issues we've had at parishes, with either toxic culture, or a difficult priest, or any other myriad of things... and yet we don't write off the church as a whole for those experiences. We acknowledge them for what they were: peculiar circumstances involving specific people. I treat the finance situation the same way.

Find a different job than music. You don’t want to work every weekend.