I think the President simply did not want Bolton around to keep speaking for the administration (which he did frequently; especially in the Middle East).
Not only is Bolton in favor of staying indefinitely in Afghanistan, reports in the Israeli press have hinted for weeks that Bolton was teaming with Netanyahu to take "bold" steps against Iran, with implied US support. There may have been an unholy alliance forming between the two that exceeded Bolton's pay grade and was outside the administration's strategy for peace in the Middle East.
I suspect this is one of the reasons the President--- for the first time---did not take the Israeli PM's phone call while at the G7, who was nervous that POTUS was going to meet with Iran (he wasn't) and wanted to talk him out of it. The Israeli press has also been taking notice that the POTUS has not made a gesture (so far) to help pull Netanyahu across the victory line in the elections scheduled next week.
By this time in the April election the President had had Netanyahu to the WH, recognized Israel's sovereignty over the Golan Heights and tweeted "hailing the special relationship" between himself and Netanyahu several times. The Trump administration made a final potential election gift to Netanyahu on April 8, hours before the polls opened in Israel, when the president officially designated Iran’s Revolutionary Guards Corps a terrorist organization. (
https://www.timesofisrael.com/trouble-in-paradise-trump-conspicuously-absent-from-netanyahus-re-election-bid/)
Bolton was effing up one of the President's and the administration's strongest alliances and relationships.
Keeping Bolton would have been worse for the administration and the country than any snarky article taking aim at the President for his decision.