Usually the fungus is not a health problem if you don't consume them. Most potting soils have been sterilized so it doesn't have fungus. Fungus usually occurs like this with the soil is too wet. You can go thru a laborious process of scooping out the fungi, taking all the soil and sterilizing it in the oven, sterilize the pot, wash off the roots of the plant and repot. Personally, I'm a little lazy for all that work. You should make sure there is good drainage on the pot so it doesn't stay waterlogged. If you have a tray under the pot, remove it. And just cut off the cap of the mushroom so the spores cannot spread. Remember that there are some good fungi also. If your seedling is still small, I would just remove it from the soil, use sterilized soil and repot it (just wash off the roots gently before repotting.