They are not harmful, actually they help in decomposing organic materials, wich then will fertilized the soil. Their presence indicated lots of moisture and many un-decomposed organic materials. For most of mature plants, this will be of no problem, and as the organic material decomposed, the fungi will disappear. However fungi produced and released enzyme to digest their substrate during fermentation as well as some other side product such as alcohols, and that could affect some "tender" plant especially seedlings.
The presence of un-decomposed organic substance will also invite many other kinds of fungi, bacterias and bugs, this in many cases will be not good for seedlings... These is among the reason people start seedling in a compost free medium. but if you want to grow an established (grown) plant.. it could be just fine.
If the fungi really dominant, then, raking the soil will make it more airy and dry faster, this will reduced fungi population. Also avoid watering to much, the last effort if needed, is to remove excess of un-decomposed organic bits such as wood chips or leaves litters, while the use of fungicide is only advisable in an urgent situation.
