How odd. Flu is a viral infection and antibiotics won't have any effect on it. I'd be surprised if any doctor would prescribe them for you. Maybe you have a bacterial infection that's giving you flu-like symptoms?
The flu jab isn't 100% effective; every winter they have to make a guess as to the strains that will spread through the UK, often based on what was rife during the previous winter in the Southern Hemisphere - which is why we've got so-called Aussie flu this winter - but sometimes they guess wrong.
To revert to your original question, I've certainly been prescribed antibiotics for an infection since being diagnosed as T2 and so far as I know, they're perfectly OK for diabetics so long as - like non diabetics - you don't have an allergy to them. Hope you are better soon.