Do they persecute their troops if they believe in their Jewish Messiah, Yeshua, Jesus? That’s a clue, AFAIC.
I'm sure there are some Jews in the IDF and Israel generally who persecute Messianic Jews - ultra-Orthodox Jews particularly. Many Jews look back on the WW2 era as a time with "Christian" Europe did nothing or was complicit in allowing the gross suffering & persecution they experienced. I can understand why some Jews disdain Messianic Jews. Having said that, Israel Jews in the IDF are mostly not ultra-Orthodox but most are more secular than religious. I would question any 'widespread' persecution of Messianic Jews in the IDF. Do you have information that would say otherwise?