Sadly this is more a symptom of how trademark law works. There's a "use it or lose it" aspect that compels brands to fiercely, overzealously defend their logo against any that look even remotely similar, or they risk losing their hold over it.
Brands don't do it for their own satisfaction; really the bad press it can generate is often enough to see any case dropped — but what matters is that they show an effort to 'defend' their trademark.
Trademarks are for a specific line of trade, though, as the name implies. Apple isn't in the fruit or food business at all as far as I know. Not sure whether this is different in the EU (or Switzerland, which I guess isn't part of the EU).
Their application doesn't list any businesses related to agriculture.