By defining the geographic scope of a future Palestinian state as the entire territory between the Jordan River and the Mediterranean Sea, the slogan encompasses the land where Israel currently exists. To remove all doubt about the context, remember that it has been widely used by groups like Hamas - whose founding charter explicitly calls for the elimination of Israel.
I'm sure there are people who use this phrase now and do not wish to destroy Israel. Just like there are people who use phrases like "all lives matter" and genuinely want racial equality. Unfortunately the terms are hard to disambiguate from the people chanting them.
Either way, we won't settle this argument now, and we don't have to. I simply do not wish to see people imprisoned for saying offensive things. That seems like an important pillar of democracy to me. I uphold the rights of people to say offensive things especially when I disagree with them. Free speech means nothing unless we're doing it when it's really hard.