At the start Mark Walberg says: "We can speculate why certain events happen but in the end we may never know."
So along with that statement and no reasoning at the end, we aren't even sure if it was an eco-friendly message. All anyone in the film was doing was speculating, we don't know why it all happened or exactly what caused it.
Even after they speculated it might be the plants, why lead the entire group through an open field of green grass & trees? Even with all the events in nature you mentioned, none of them just happen for no reason or simply dissapate in thin air after it's done.
We as a species speculate on a great number of things.
Is global warming, this cycle(some say we've cooled but I digress), being impacted by man? Is the ozone hole really an issue or does it fluctuate naturally? Were the plants the villains or something else?
Speculation and a cavalcade of voices makes many think man is having an adverse impact on the planets climate. As a society we banned certain chemicals cause some science heads speculated they might be causing holes in the ozone. Elliot(Whalberg) and the talking heads on TV speculated plants might be the bad guy so that is the narrative path M.Night took us on.
What if for all our self percieved intelligence there are just things we can't grasp? What if Global Warming/Cooling and the Ozone are beyond our full understanding? Likewise we created a boogeyman out of nature in The Happening
cause it was our perceptions that said, nature was the dominant constant. Parks. Fields.
As a species our great minds said the solar system revolved around the planet Earth. That the Earth was flat. That you could sail from Spain and end up in India without hitting land. There aren't any measurable units smaller than an atom. We could go on and on.
"...in the end we may never know", to use your Elliot statement, what M.Night is truly trying to convey. Eco-friendly or Eco-indifferent. Maybe its not even entirely an eco message at all. Maybe its something else entirely.
That is part of what I like about this and Lady in the Water
. The viewer can take different messages from it and some viewers may not take away the same things. I don't like vagueness in all my movies but its why I enjoy M.Nights movies as a break from the cut and dry straight forwardness of nearly all other movies.
Some people are just not wired to enjoy this type of storytelling and hence the backlash I think.