This movie cannot be pro-faith
I'm not sure if this has been mentioned already in another thread.
The reason that this story cannot be compared to the faith vs. atheism debate is that the movie seems to actually be pro-science!
1. Consider the very nature of what Horton knew/believed. His claim was NOT something unscientific or "magical." He did not claim that an entity was omnipotent and had control over everything. He basically was talking about a colony of life that existed at a microscopic level.
2. On the other end, the Whos' situation seems a little bit more comparable, since their mayor describes Horton as being "in the sky" and "invisible." But still, he is not claiming anything supernatural. He turns to a SCIENTIST who verifies that it is possible for them to be living on a speck flying through the air, and he uses a SCIENTIFIC method for being able to hear and speak to Horton.
3. The conflicts and resolutions are also science-based. The reason Horton is the only one who can hear the mayor is because of his genetic hearing ability, not because he is a "chosen one." When Horton fails to speak to the people after the mayor promises it, it is because Horton is a mortal being who can temporarily lose control of the speck, not because "Horton works in mysterious ways" or because the citizens of Whoville are "not spiritual enough to hear him." The Whos resolve their problem at the end by increasing the level of noise they are making (mostly thanks to the scientific-minded son of the mayor). Notice that they don't resolve the problem by simply "believing strongly" or by holding some kind of mass prayer to the elephant.
Anyway, perhaps the filmmakers may have wanted to present a pro-faith argument, but the product doesn't work out that way. In fact, the persecution of Horton (and the mayor) seemed similar to attacks on Socrates and Copernicus, both of whom promoted knowledge and thinking over blind faith in accepted beliefs.