"She does not see it."
Translation:Ona tego nie widzi.
You asked here why there wasn't any change to Genitive, and I answered there often (usually?) is, but not with absolutely every verb. But here it definitely does. So when 'widzieć', which takes accusative, is negated and starts being 'nie widzieć', it gets the genitive, and genitive for 'to' (and also for 'ten') is 'tego'. Better focus on finding the rarer examples when this does not happen.
"to" is a dummy pronoun, it has a different function.
"ono" theoretically is the neuter equivalent of "on"/"ona", but in fact it's rarely used. After all, what could it refer to? Using on/ona/ono to denote animals is rare, so it leaves us with about two nouns: dziecko (child) and niemowlę (baby). And it feels more natural to precise the subject anyway. Or the gender, at least.
Grammatically, 'on' for pies and 'ona' for łyżka would work, but that's just very strange. I wouldn't use any pronoun at all. I would just answer "Jest w pokoju/Jest na stole", or even omit 'jest' as this is just a short answer. Alternatively, I would rather repeat the subject instead of using any pronoun.
"to" just wouldn't work.
Yeah, you wouldn't say "To jest czerwony".
In English you'd answer "It is red", right? But "To jest czerwony" means at the same time "It is red", "This is red" and "That is red". Therefore the real meaning is basically the same as saying "[This/That/It] is the color red", as if you were explaining the names of colors to a child.
"To jest samochód" makes sense, because all of: "[This/That/It] is a car" make sense. Basically, the difference here is between a noun and an adjective.
Yes, "widzieć" takes Accusative ("Ona je widzi" = "She sees them" if 'them' refers to a 'not masculine-personal' noun or "She sees it" if this 'it' is neuter in Polish), but if you negate a verb that takes Accusative, it takes Genitive instead.
This is the only case which changes when negated, other cases stay unchanged.
Here's an excellent reference I usually have open at all times: https://en.wiktionary.org/wiki/Appendix:Polish_pronouns