McDonalds did not officially endorse Israel. The franchise owner of all the McDonalds restaurants in Israel did. McDonalds corporate did not approve the message although it seems like it did not really matter what the facts were. (https://www.theguardian.com/business/2024/apr/05/mcdonalds-i...)
everyone takes a side on everything. explicitly or implicitly. intentionally or unintentionally. due to the interconnected nature of the world, it is impossible to construct a true-neutral position. the appearance of neutrality becomes more difficult the more important an issue is to those you interact with.
so, it's not really well-defined to ask whether or not a coffee shop "should" be taking sides, it will take one in all situations. it is a (slightly) more tractable question to ask "how should a coffee shop take a side?" Given how difficult this question is to answer still, I like to answer it with, "doing good is generally aligned with the long-term profit-motive."
this is also why boycotts are actually useful! though collective action, you can align the profit-motive with "good" clearly. this makes it easier for a coffee shop to move in-line.
Apparently not all that pro-Palestine, if Wikipedia is to be believed:
> At the end of 2023, five employees were sent home from the Gilman Street location for wearing Pro-Palestine pins. Despite asking for a written statement from management about why the pins were not allowed, the employees never received any information from management. The employees were sent home and the entire staff unionized.
The founders immigrated from Palestine so that's not surprising. They even donate a portion of proceeds to Palestinian aid efforts. Surprised to see they are going under though. They have been a grocery store staple for a while.
In my experience around the SF bay area the vast majority of local or independent coffee shops have a Palestinian flag or stand with Palestine poster right on the front glass.
While I think that your choice in coffee shop has little to no effect on the actual Palestinian country or people, you can always try going local instead of supporting these multi million dollar chains.