The OP didn’t mention any specific group, only that the flag was flying outside Christian churches. You wrote, “This would almost never be done by a mainstream Church unless it was a congregation of Messianic Jews or some other like denomination that felt Christians supplanted Jews or Israel in some form.” The way I read this sentence, it meant that you believe the only mainstream churches that would fly an Israeli flag would be those that believed Christians had supplanted the Jewish people. This is incorrect since evangelical Christians who are pro-Israel are pro-Israel specifically because they believe that the Church never supplanted the nation of Israel.
You may already know this, but I wanted to clarify that supplanting Israel is not the only reason that a Christian church, mainstream or not, would fly an Israeli flag.