Air conditioning is well established as a potential source of fungal spores in the air of buildings. The units tend to get wet as warm moist air hits cold cooling surfaces, and if that moisture is not efficiently drained away then conditions for fungal growth are quickly established - along with a highly populated source of fungal spores in the warm air that is sucked into the unit.
A car warranty company has recently released a reiteration of established advice to car owners on the best use of air conditioning units in cars to avoid a face-full (or perhaps more sinisterly a lung-full) of spores. They make the point that in these days of high fuel prices people will be more inclined to switch the air-con off in their cars to save on fuel use (an air-con unit can increase fuel consumption by 10-15%).
If air con is left on the assumption is that there will be a steady flow of spores, but if it is switched off for a period of time the spores will build up and be released in a far more concentrated cloud when the unit is activated.
I would say that the situation is more complicated than that - there will only be a problem if the air con unit remains wet for some time for example. Some interesting points are made in this article and some guidance to avoiding fungal contamination of your car air-con is given.
The dynamics of mould contamination from car air-con's is examined in the scientific paper entitled "Effect of air-conditioner on fungal contamination".
The main findings seem to be that using your air conditioning for more than 20 days in the summer increases the amount of fungi in the air of that car some 400% over not using it at all, but less regular use increases that figure only a further 50% (Table 4).After the first blast the amount of fungal spores drops 75% over the next 10 mins (Table 2).
One in four cars tested had 1000 spores per cubic metre of air, while one in eight had over 2000 spores per cubic metre - pretty high figures for a person suffering allergies, ABPA or immune compromised.
Take home message is that if you are vulnerable to fungal spores, rather than run it more frequently turn your car air conditioning off completely. If you must keep cool pay for careful maintenance of the unit and/or ensure HEPA grade filtering is in place!