The title of the song is a phrase that appears twice in the Hebrew Bible, originally in a negative sense of ‘these things you [=the Israelites, or humanity in general] are culpable for’: Jeremiah 2:34, Ecclesiastes 11:9.
The line ‘over the honey and the stinger’ is a similar inversion of a common phrase: ‘[one tells the hornet (sīc):] none of your honey and none of your sting’, i.e., the whole package of drawbacks and potential benefits someone or something might entail are unecessary. The phrase comes from Tanhuma on Balak.
The line ‘Don’t uproot that which is planted [=נָטוּעַ]’ (not a ‘sapling’) is a reference to Ecclesiastes 3:2, and is also seen as a political reference: Shemer said the song was written to comfort her recently widowed younger sister Ruth Nussbaum, but it seems to have also been, in part, a protest against uprooting Israeli settlements, specifically from the Sinai Peninsula, a group she was personally friends with. An earlier version of the song, which she quoted before the song’s premiere, is even more explicit about this:
Over all of these, over all of these
Spread your sukkah of peace;
Do not uproot that which is planted,
Do not destroy my home.
She altered these lyrics afterwards, but the song still became a de facto anthem for Gush Emunim protests against evacuating Yamit and later Gush Katif. She did not oppose this adoption, but the song’s original performer, Yossi Banai, did so vocally.
Finally, the song contains one more Biblical reference: ‘May you return me, and may I return’ is a reference to Jeremiah 31:17.
His brother's name was Jubal; he was the father of all
who play stringed instruments and pipes. (Genesis 4:21)