Do they still operate or are they remnants of pre-revolutionary times? I don't see how they can operate in a state whose publicly stated goal is to "wipe Israel from the face of the Earth".
Iran's issue with Israel is not related to Judaism.
It's important to distinguish between anti-zionism and anti-semitism. Iran is the former but not the latter.
The article has several paragraphs on the synagogues and how they operate today. Jews were wearing skullcaps in the streets and there were apparently several operating synagogues.
The article also mentioned that the buildings are unadorned from the outside, and that the website for the synagogue he attended had text on it condemning the Israeli government for the 2008 Gaza atrocities, so it's not completely unencumbered.
Iranians I've talked to say they have no problem with Judaism. Their issue is Zionism. The distinction is lost in the West but not in the Middle East. Arab Jews who were forced to leave their countries for Israel had a hard time integrating into Israel and there are still problems in Israel over this as I understand it.
Do they still operate or are they remnants of pre-revolutionary times? I don't see how they can operate in a state whose publicly stated goal is to "wipe Israel from the face of the Earth".