Daisy, covering them is likely to increase the chances of fungal problems. Unless you want to spray, air circulation is one of the best means of minimising the chances of infection. If the air is moving, the fungal spores are more likely to keep moving and not settle. Still air, particularly still and humid air, is a fungal spore's best friend.
It's also a good idea to aid air circulation by selectively thinning the foliage to prevent clumps of impenetrable foliage forming.
If you don't have fungal problems at the moment, it's unlikely that any infection that arrives in the near future will bother your plants. It takes a long time for the most common fungal diseases - Early Blight, Septoria Leaf Spot, etc - to cause serious problems. In fact, the end of the growing season and the arrival of cold weather usually wipes out a plant before a common fungal disease does.