Except it's not, it's a call to end segregation and create one free, secular and democratic nation across the entirety of the original territory of Mandatory Palestine. Apartheid South Africa also segregated native peoples into tiny enclaves as a form of democratic suppression, and that was resolved by creating one free and democratic nation:

That's part of why South Africa was the nation that brought charges of genocide against the Palestinians to the ICC. It's also why outspoken zionists like Elon Musk have recently tried to condemn "racism against white people" in South Africa.

Edit: I will say, you are correct that both sides use it, though Palestinians (and their allies) will always include "Palestine will be free" at the end, and that supports my above statement. However, when the Israeli side uses it, they make clear that the one nation would be Israel, which is specifically a Jewish state to the exclusion of other religions.

It is an emancipatory slogan that calls for an end to apartheid and for equal rights.

Yousef Munayyer, head of the Palestine-Israel program at the Arab Center Washington D.C., has written extensively about the meaning of the slogan before and since Hamas's attacks on Oct. 7, which led to Israel's current bombardment of the Gaza Strip.

"It's an expression of Palestinian nationalism and it's an expression of a demand for Palestinian freedom or self-determination," said Waxman. "I think Palestinian self-determination need not come at the expense of Jewish self-determination. Nor do I think Palestinian freedom has to be considered a threat to Jewish rights."

• https://www.cbc.ca/news/world/from-the-river-to-the-sea-palestine-1.7033881

Simply put, the majority of Palestinians who use this phrase do so because they believe that, in 10 short words, it sums up their personal ties, their national rights and their vision for the land they call Palestine. And while attempts to police the slogan’s use may come from a place of genuine concern, there is a risk that tarring the slogan as antisemitic – and therefore beyond the pale – taps into a longer history of attempts to silence Palestinian voices.

• https://theconversation.com/from-the-river-to-the-sea-a-palestinian-historian-explores-the-meaning-and-intent-of-scrutinized-slogan-217491

The use of the phrase “from the river to the sea” has come under particular scrutiny in the last three months. When Palestinians, or anyone on the left, has used the phrase to demand a free Palestine—as in the popular chant, “From the river to the sea, Palestine will be free”—those on the right have disingenuously argued that it is calling for the death of all Jewish people in Israel.

• https://newrepublic.com/post/178243/benjamin-netanyahu-literally-says-from-the-river-to-the-sea

In 2021, the Palestinian-American writer Yousef Munayyer argued that those who saw genocidal ambition in the phrase, or indeed an unambiguous desire for the destruction of Israel, did so due to their own Islamophobia.

It was instead, he argued, merely a way to express a desire for a state in which “Palestinians can live in their homeland as free and equal citizens, neither dominated by others nor dominating them”.

• https://www.theguardian.com/world/2023/oct/31/from-the-river-to-the-sea-where-does-the-slogan-come-from-and-what-does-it-mean-israel-palestine

Preventing any possibility of a Palestinian state has always been Israel’s policy, one that the settlement building in the Occupied Territories is meant to ensure. This policy has been intensified under Benjamin Netanyahu, who in January 2024 publicly vowed to resist any attempt to create a Palestinian state and to maintain Israeli control from the river to the sea.

It is often maintained that the slogan ‘From the river to the sea, Palestine will be free’ expresses a genocidal and antisemitic intention. But this is generally not the case. On the contrary, the slogan has historically been used to articulate a wide variety of political strategies for Palestinian liberation

Denying such demands seems as self-evident to most Israeli Jews as the air they breathe. It is this denial that has led to the dehumanization of Palestinians and has culminated in the genocidal mood that is prevailing in Israeli Jewish society today and in the assault taking place now in Gaza. This should be viewed as the real problem and not the legitimate chant of ‘from the river to the sea: Palestine will be free’.

• https://revdem.ceu.edu/2024/03/27/from-the-river-to-the-sea-one-slogan-many-meanings/

Palestinians being free is not at all the equivalent to genociding israelis. Although thats the sick way israels think.

"both sides"