Not all the fungi you see in the garden are bad. Have you noticed unusual shapes, growths and bright colours amongst soil and leaf litter? There are the decomposers of the plant world, without them there would be little breaking down of organic matter in gardens and natural areas.
These are not harmful to plants and will be beneficial to the garden in the long term. The organic matter they are feeding on breaks down and is converted into nutrients in a form plants can absorb.