A few notes and responses...

People have always had a religious or quasi-religious reverence for nature. In modern times, some people have started to see nature more as an enemy to be conquered than as a god to be worshiped.

Evidence please? I had thought this was merely part of the myth of the Noble Savage. Some people have had nature-oriented religions, but plenty of others haven't.

More importantly, people started to see nature as something to be conquered at precisely the point that people gained the numbers, technology, and profit motive to do so. That people didn't try to conquer nature before that, when they 1) couldn't and 2) had no reason to do so, proves nothing. Going forward, the ability and desire won't disappear, so any comparison is misleading.

I think the objection would be without merit if one were to broaden the scope of concern to something like all creatures, present and future, capable of having experiences (who else is there to care about?)

You seem to assume that such broadening would be somehow right or justified (morally? expirentially?) but without a good argument, many people don't accept that - and legitimately so, I feel.

A third response is that getting into a "conquer nature" frame of mind puts people into a "conquer everything" frame of mind and leads to aggression against other people. This might have merit historically

I think that the causal relationship, such as it is, is the other way around - especially historically. Because people were in a "conquering" frame of mind about all other people and things - notably the people living "in nature" - they also naturally proceeded to conquer nature.

So what, if anything, is left to the idea that there is something special about nature worthy of particular regard? And by special I mean something beyond the fact that many people just plain enjoy it

Why do you need something more special than that? I think all meaning and value should ultimately derive from people just plain enjoying things :-)

when you are in nature or contemplating nature, you can be confident that the resulting thoughts and feelings are uncontaminated...

That would require some massive weight of evidence to prove it. A priori, all of your thoughts and feelings about everything you encounter are pretty much determined by all those things whose "contamination" you fear - up to individual variation, of course.

When you look at a waterfall and you like it...

But what about when I look at a waterfall and I don't like it? What if I think that, in fact, it would be nice if some park employees came along and cleared a proper trail from the parking lot and put down some benches? Are you going to claim that I'm "contaminated" and need to be cleansed... er, deprogrammed? Or is preservation of wild nature more important than such opinions which are held by some people?

I realize you don't say this, but it's the logical outcome of your ideas...