Generally speaking: Spain, Italy, Austria, France and Switzerland prevented the US from using its airbases or airspaces to transit their planes to the Middle East.
The UK at times also blocked use of its air bases.
France probably cut a separate deal with Iran, evident from the release of the French hostages, the call Macron had with the Iranian FM and the fact Iran lets their ship cross
At the beginning it was fairly clear to everyone outside the US that this was an illegal war of aggression. That we waited until Iran had struck Israel and gulf countries was at least a fig leaf for the pretence we were doing something reasonable.
What source do you have for French ships being allowed to pass?