That's not entirely true. In recent years, at least in North America, HPV vaccines have become a significant ideological issue, mostly for purely moral reasons. (Though the media exposure of this controversy seems to have died down somewhat recently.) I haven't followed this issue in much detail, however I've noticed that it has involved not only moral disputes, but also disputes about factual questions that are in principle amenable to scientific resolution, but the discourse is hopelessly poisoned by ideological passions.

What you write is true about the majority of the historical vaccination controversies, though.