Gyratory traffic schemes, extended one - way systems etc

I forgot to reply directly to this bit. It's nonsense because you can't single out buses as the greatest perception of danger-creating cause. People don't tend to distinguish much between different kinds of motor vehicles when they complain about their general perception of danger, they just cite all kinds of motor vehicles. When they do make specific complaints, e.g. on pretty much any cycling forum, or when talking to people at stalls, the main complaints are about taxis, minicabs, or private cars. Buses are in the mix, but not very frequently.

That's better. A proper argument :-)
However if, as we are, you were discussing a scheme which was specifically about buses sharing a road with cycles and you asked the same questions you would get a higher number of people singling out buses rather than vehicles in general. I expect bus speeds on such a road would be a lot higher for example, so it's likely that the perception of danger would increase substantially.

I linked to the article, by the way, because it was a decent argument in favour of the proposition that the perception of cycling safety is enhanced when there aren't buses (or any other heavy traffic), to which "simply nonsense" was not an adequate riposte.

Buses carry something like 50% of London's road traffic by passengers. If you were to divide the number of bus/cycle crashes by passenger trips and compare that to the number of motorcycle/cycle crashes by motorcycle trips and you will see that the former number will be much lower. Unlike motorcycling, buses are a highly capacious and effective mode of urban transport (obviously still not anywhere near as good as cycling).

This is a sound argument, but it's an answer to a different question.
Dividing the number of collisions by passenger trips is irrelevant to the two questions that matter when you need to find out about cyclist's perception of danger. These questions are "as a cyclist are you more likely to be hit by a bus or a motorcycle" and "if you are hit by a bus, are you more or less likely to be killed or seriously injured than if you are hit by a motorcycle". I believe that the answer to both these questions points to the bus as the bigger perceived (and actual) risk.