The stated moral of this story is “a person is a person no matter how small” or everybody matters.
But the real read I get off the story is anti-atheist or anti-skeptic, pro spiritual.
“if you can’t see it, it doesn’t exist!”-Said the villain.
Anyone else feel the same?
Alternate interpretation, it is about germ theory 
And you put the period in exactly the right place. That’s what it’s about.
If you want more depth, read up on Geisel’s early days - I recommend *Dr. Seuss Goes to War *- and you’ll see that he was aligned with the far left in the prewar/wartime era. I would read more about government/social oppression than anti-atheist/pro-spiritual viewpoint into Horton.
(See, in particular, his cartoon for PM “But they were foreign children, so it didn’t really matter” included and discussed in Goes to War.)
But Horton can hear it. Horton isn’t the hero of the story because he believes in something he can’t tell is there. He knows based on his own senses that the Whos are real. He’s the hero of the story because he’s willing to stand up for them even when it makes himself look foolish, and even in the face of the abuse and derision of the other animals.
Also, for what its worth the other animals behavior would be villainous even if Horton were completely delusional. The other animals could just say “That Horton is a little nuts, but whatever, let him have his flower with his imaginary people on it.” Instead they lock Horton up and try to boil the flower, for no other reason than because it makes them angry that Horton believes something they don’t. If it were about religion, the other animals behavior would be equivalent to defiling someone’s sacred artifacts and throwing the believers in jail.
In other words, if it were about religion, then it’s not anti-atheist, it’s anti-religious persecution.
It’s also not about abortion, despite many attempts to make it so.
In a Seuss book? Hardly.
The others said “Horton has surely gone nuts,
No ifs, no howevers and clearly no buts.
But leave him alone, it’s doing no harm
When voices tell him to kill, we’ll be alarmed.”
Nice movie, by the way.
Well, it is a current trend, I guess. You’re supposed to be deeper if you rely on more than the scientific method. It’s partly true, I guess. I’m not sure we should judge a movie by its character’s lines though.
How is it anti-skeptic? The other animals insist the Whos can’t be real because they’re outside the realm of their own experience, they act like intolerant jerks, and Horton is vindicated because the facts are on his side. The story says you should treat everybody nicely no matter what they look like and it suggests that in the end the truth will out.
I thought it was supposed to be a primer to the concept of infinite recursion. Especially when I watched the end of the animated version (go ahead and skip the ad; it will take you to the relevant portion).
Fun fact: I once wrote a SF short story on the subject, and named my protagonist Nick* Horton.
*“Nick” for Copernicus; get it?
I’ve watched The Grinch/Horton special plenty of times, but not until this year did I realize that How the Grinch Stole Christmas takes place on the dust speck Horton finds.
“I tried and I tried but they won’t hear the news.
All of them doubt the existence of Whos.
The voices tell me how to fix up this jam;
Load up my Magnum, son-of-Sam I am.”