Beetle,
If it helps, I was very sceptical about the flu jab and the whooping cough jab when pregnant. I was so protective over my ivf baby I couldn't bear the possibility of these jabs causing it any harm. My son developed ITP (where body destroys it's own platelets and you can bleed uncontrollably) from his MMR booster, so I was more wary than many.
But, when I was 11 weeks it was January and flu was widely about and there were loads of ladies on the forums in America particularly who caught it because they were anti vaccination. The consequences of having flu while pregnant were far worse than the possible side effects of the jab, so I gave myself a mental slap round the face, told myself to stop being so cynical of the medical profession and got on with it.
I didn't catch flu and my baby is here unaffected.
Likewise, because whooping cough vaccination is quite recent and there is minimal evidence that it works, I asked my consultant. He assured me that the stats collected over the past few years show no correlation between the vaccination and increased third trimester problems, so to go ahead. I had it within a few days as I am in London, which is highest risk.
Again, baby was totally unaffected (other than the fact I got a headache immediately after the jab and he went rather quiet for a few hours but was moving as normal by next day).
Babies are very vulnerable if they get whooping cough, it really is nasty. My dad caught it as a kid and he said it is the one illness he remembers because it was so awful. He couldn't breathe for days. I knew I would never forgive myself if my baby caught it and I had to watch him fight for breath.
It is of course a personal decision, but I hope my experience helps reassure you.