Umm, you already answered your own question. It depends on the game. Unfortunately visual novels have pornographic conotations, but that bad reputation isn't totally fair because not all VNs are nukige with sex scenes, much less eroge-- where the only purpose of the game is graphic sex scenes. Throwing out visual novels as a "dangerous" medium just because of those games would be like throwing out all traditional romance novels as a Christian just because some of them are erotic fiction. You just need to be extra careful with what you consume. Read reviews, stay on sites that are clean, don't buy from MangaGamer. Don't apply "adult" patches to VNs you buy on Steam.
As for Tokyo School Life in particular, I have not played it yet. It has some mild fan service-- girls in swimsuits, you can see how "bad" it is on the sceenshots page of the game. Nothing really inappropriate; just the sort of stuff you'd see in your typical moe anime. There's no adult content, and since the premise seems to be "Go to a school in Japan and learn Japanese and about Japanese culture by talking to young cute school girls doing cute things" I can't imagine it having extreme violence, problematic religious themes, or heavy-handed nihilistic depressing stuff you might get out of a darker VN.
Just research the VNs beforehand to see if they're clean rather than wondering if VNs in general are "okay," it can be just like any other fiction.
I've been thinking that maybe I should do a content review for all the VNs on Steam, if anyone would find such a thing useful. Owning all the Steam VNs is one of my goals.
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