I think it's also very location specific.
I grew up fishing the NC and NW parts of the state. To be quite honest, fly fishermen were rare until you got as far east as the 1st Fork/Kettle/Pine drainages. You saw one here and there, but there was nowhere that they outnumbered bait fishermen.
The switch from bait to fly gear was not the typical path there. Bait fishermen simply got better and more experienced with time. And as a result, they were more likely to C&R, less likely to cause mortality, more likely to focus on wild trout, etc. The same things we associate with flyfishing. I spent a few 1st days in a row without seeing a single stocked trout put on a stringer, everyone was C&R.
Then I moved to State College and eventually SE PA. Fly fishing was MUCH more common than I was used to. And there weren't very many experienced bait fishermen, they merely switched to fly gear once they got to a certain point. And I did the same. So the less experienced and less interested made up a much higher % of the bait fishermen, and the more experienced type was rare.
I believe the negative stereotypes we associate with "bait fishing" aren't so much indicative of the tackle choice, they are indicative of level of experience and/or interest in trout fishing. In short, we hate beginners and those that aren't as into it as we are. Those who think that trout come from trucks, who think you should keep all the fish you catch, who are unconcerned about a fish's survival if they do release, etc. And to be fair, those things are damaging to fisheries. Of course, we can't eliminate opportunities for beginners, because some portion of those will eventually get into the sport and become the stewards of the waters that we want them ALL to be.
So what do you do? IMO, you protect the streams that need protecting. Those that are popular enough to be harmed, you limit harvest and mortality with regulation. But only to the degree necessary, as you want to leave as many open to the bait crowd as possible, and when you do have regulations, you make them as non-restrictive as you can. For instance, if you can get away with it without overly harming the fishery, AT C&R is better than ALO C&R is better than FFO. Thus, by making it a smaller step, you are inviting those beginners to grow as fishermen and conservationists.
At least that's my take. I do think TAP is probably misguided to an extent. But I also think some other organizations may be as well, and TAP is nothing more than a counter to that. With good intentions, our hero organizations push fly gear, FFO projects, and the like, forgetting that there still exists in many areas an experienced and overall good group of bait anglers. You can say TU welcomes bait and spin fishermen. And that's true. However, they certainly make no attempt to market to them. The calendar is full of fly fishing pictures, the gifts are fly gear, etc. When's the last time a sign up gift was a fancy spinning reel or a box of rooster tails in various sizes and colors? When's the last time in trout magazine there was a story about methods of working live minnows, or the ads included the newest and greatest mono line made by Berkely, Stren, or Silver Thread? When's the last time you saw a picture of a guy sitting at a desk, but instead of a vice and fly tying stuff, there was spinner making equipment? Or how about at the meetings, how many speakers concentrate on spin or bait fishing topics? You're kidding yourself if you think it's a welcoming environment for the more avid bait and spin fishing crowd.