What the song is ACTUALLY ABOUT IS THIS: Israel is the only Arab country with nukes, and that should scare the bejeezus out of us.
Now you might think: Hey, random guy! 1.) How the hell do you know that to be true? 2.) Anti-semite! 3.) What's so wrong with israel?
Let's start with a distinction: Israel and Jewish people are DISTINCT IDENTITIES. You can be an Israel Jew, and you can be a non-Jewish Israeli, and you can be a non-Israeli Jew.
Now, here's why this song IS NOT JUST ABOUT WW2:
Listen to the tone of the song:
"cryin' bout the burnings back in world war 2's" "little children with doves on their shoulders, their eyes rolled back in ecstasy"
Now if this song, as you guys indicate, was supposed to be about how bad Israel got shafted in WW2, those lines would not only be disrespectful but not even funny.
Let's not forget that Israel became a country in 1948 by waltzing into Palestine and annexing land as they saw fit, claiming that what happened to Jewish people during World War 2 justifies taking land from other people. Israel has gone to war with its Arab neighbors 7 times between 1948 and now. In fact, this album was written between 1967 and 1968, immediately following the Six-Days War between Israel and Egypt, Jordan & Syria. Captain Beefheart used to hang out with Frank Zappa a lot. Frank Zappa's music was very influenced by the politics of the day. Israel is widely believed to have developed nuclear weapons in the late 60s, also right when this album was being written. This makes it almost certain that Captain Beefheart, someone who was politically conscious thanks to Frank Zappa, was aware of Israel's "bully status".
Now that we've seen that Israel is a bit of a bully, examine the line "their eyes rolled back in ecstasy" - three things should make you suspicious that this song is not just about how bad the Jews got it from Hitler:
1.) Ecstasy is NOT SOMETHING VICTIMS EXPERIENCE (so that rules out the song being about ww2).
2.) Their eyes are rolled back in ecstasy is clearly referring to that Pentacostal brand of religious intoxication.
3.) They're begging the Lord not to let THEIR OWN FINGER launch the FIRST STRIKE that will start WW3. If this song was about Holocaust survivors, shouldn't they be begging the Lord to stop OTHER PEOPLE from launching?
Therefore, the song is about Israel being aggressive and territorial - Israel is depicted as young children with doves on their shoulders, asking god to prevent them from nuking their Arab neighbors for fun; and should we dare call Israel on this monstrous behavior, they raise the cry of ANTI-SEMITE - notice the lyrics say STILL cryin' bout the burnins back in WW2 - this means the cryin' has been going on and on. The "one mad man, six million lose" line? That's referring to how Israel's (then-)current behavior cheapens the plight Hitler put them through.
The real message of this song then is this: "Hey, rest of the world! Israel here. We'll nuke (= burn millions of) our Arab neighbors if we feel like it, but it's ok because Hitler did it to us first!"