The Good Dinosaur is Pixar’s MBM. It’s a fun, fast paced, entertaining film, well made and technically flawless.
Why it stumbled is a good question, and I think there are probably several overlapping issues.
First off, while one of the things the movie does perfectly is convey about 90% of the story in purely visual terms, I don’t think many in the audience grasp that the film is supposed to be happening in the present day, specifically in an alternate timeline in which dinosaurs didn’t die out but achieved sentience and Neolithic technology.
Even supposedly scientifically literate people have failed to understand that, complaining that the movie mixes dinos and cavemen.
Well, no: The film is not set 65 million years ago (except for the brief opening gag) but Right Now.
But that leads to problem #2: The world of The Good Dinosaur looks absolutely realistic, some of the best nature effects ever put in a film, but the character design on the dinos is much too cartoony for the world they inhabit.
One may argue over 65 million years that dinos would evolve into odd forms even as they were acquiring intelligence, but they still seem more suitable for The Flintstones.
The third problem is script oriented: Pixar films traditionally are delightfully complex and multi-leveled. Kids can enjoy the basic story line / characters / gags but there’s enough depth / meat for adults. Inside Out is perhaps the most perfect example of this, but the Toy Story movies and Brave are also good examples.
But The Good Dinosaur is rather plain and simple; everything is out there in full view. Scratch these characters and you find just more of what you’ve already seen.
The plot, while working for a specific goal, is still pretty episodic and any number of sequences could be dropped / rearranged / swapped out without affecting the story in total.
There’s nothing wrong with that, but there’s nothing exceptionally compelling about it. To me, that’s what makes this Pixar’s MBM: It’s good enough but not really memorable.
And finally, there’s a fourth element, one that can’t be easily quantified but one I suspected worked against the film’s box office success.
Before the movie begins, there’s a short film called Sanjay’s Super Team about a little Hindu boy whose love for superheroes is at odds with his father’s desire for him to participate in the family’s faith. It gets resolved in seven short minutes, of course, with young Sanjay realizing the Hindu deities Vishnu, Durga, and Hanuman are analogous to the Western superheroes he idolizes.
There are a lot of potential ticket buyers in the Bible belt who are doubtlessly taken aback by a sympathetic -- and informed -- view of a non-Judeo-Christian theology.
Then, in the film itself, there are several pterodactyls who literally worship a rolling storm front that they follow, preying on victims they find trapped in the wreckage the storm leaves behind.
The language and terms the pterodactyls use is very clearly evocative of evangelical rhetoric, and while one can find parallels between them and certain televangelists, I wonder if other Christians in the audience don’t perceive it as a criticism of Christianity as a whole.
This, combined with the other points mentioned above, may have kept a big segment of the early audience from recommending the film as highly as they might have.
No one factor is sufficient to sink the film on itself, of course, but together they may have served as force multipliers that worked against The Good Dinosaur.
Which is a pity, because even for the areas where they don’t hit a home run, Pixar is still batting solid doubles and triples.
 Which, frankly, would make for a helluva an interesting movie if more time had been spent on examining what that culture would be like instead of just focusing on a few isolated individuals.
 I know many Christian artists and creators who strive to do Christian superhero stories. I’m not one to say to another what shouldn’t / couldn’t be done, but for me personally I’ve always had a problem reconciling the inherent violence of superheroics with the explicit non-violence taught by Christ. But where Christianity hinges on Jesus being an actual historical person (such as the Buddha or Muhammad), Hinduism seems more open to metaphorical interpretation, and so the violent / war-like aspects of certain Hindu deities does not necessarily equate to real life militarism.