Well I have grandchildren age 7 and 9 years old and I've watched SpongeBob with them so we must all be really thick because it never occurred to me that there was some hidden meaning nor did they ever indicate they took it at anything but surface value.
Children have active imaginations and at 4 years old they're just starting to learn the difference between the true and untrue it's part of their mental development.
We can look for evil and any movie or story and find something that could be interpreted as such but that does not mean it is so.
Though most educational psychologists would agree with the ideology that some kids are too young to ''know'' certain things, I can state blatantly that the education of a child rests on the parents. For example, my daughter knows not to tell lies, and even the simplest of lies does not go by uncorrected with me. What has this led to? My daughter being so blatantly honest that she will tell me while I'm in the shower that she is going to flush the toilet and turn on the faucet so I get all hot water. lol If she comprehends such laws of action and reaction do you really think a 3 year old is too young to understand basic bad attitudes, superstitions, and drama portrayed in most modern children's animations? This is why my husband and I typically only let her watch programs such as Leap Frog, Special Agent Oso, and Curious George. If she does watch something that begins to portray something fearful, violent, angry, grumpy, disrespectful, etc. I simply explain to her, based on the situation, why what the person did was bad and how the consequences could/should/would play out. She finds Scooby Doo quite funny, but I don't let her watch it on the basis that new Scooby Doo is mostly cultic trash. Sometimes even Tom and Jerry starts a dissertation on why Tom always gets consequences (he's always trying to be mean to Jerry) and why Jerry is wrong to sometimes start trouble with him. She's going to have a baby sister soon, and little understanding of consequences and why one should not goad another will be invaluable.
Spongebob Squarepants, The Regular Show, Shake it Up, and even Sesame Street are programs that take so much backstory and commentary that my little Chickadee just isn't exposed to them. Try explaining to a little girl who you are teaching to be polite to her elders that farting in someone's face is not acceptable, or being grouchy with everyone ''just because that's me'' is objectionable when the writing is painting such things as comical.