These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Designated Villain: The Zookeeper. All he wants is to keep the penguins safe. He believes that Mr. Popper is not fit to raise the penguins in his apartment and is constantly trying to take the penguins from home. Although the law and common sense are on his side, the movie portrays him as the villain. Though partly justified as he has lied about his intentions with the penguins, such as trading them off to other zoos and splitting them up, even removing the chicks from their parents, and has repeatedly demonstrated that he doesn't think of the penguins as anything more than dumb animals, considering them incapable of love.
Mr. Popper himself in a brief scene when, out of panic thinking he really is harming the bird by keeping them, lets the keeper have them. His family treats him like he'd gotten rid of them out of spite (on the other hand, to ignore his grief he did try to act like the birds were never there)
Strawman Has a Point: Also the zookeeper, when he tells Popper that he can't take care of the penguins. Also inverted when he suggests that a single unhatched egg is proof that Popper is hurting them, which is taken as a good point, when it's really not.