This is also a sign too me that the natural soil microorginisms are not doing there job. Mushrooms are a fungi, but it is not the strongest fungi and should not be winning the battle. I would try making a worm casting tea in order to inoculate your soil with a new batch of micro orginisms.
It is not bad to have bacteria and fungi in your soil or growing medium, it is actually beneficial, but they must be the correct type of fungi.
King bud is right that certain types of fungi form symbiotic relationships with plants roots but it is not mushrooms it is endo and ecto mychorrizae. These can improve the surface area of the roots by up to 700%, they also fight disease and pathegens as well as storing nutes for later consumption by the roots. They also will help the roots survive a drought better because they store water and nutes and process it before they pass it too the roots, this breaks the ionic bonds and makes the nutes more readily availible to plants roots.
Bacteria and fungi are the most important aspect of organic growing, but will also work wonders in chemically feed mediums as well
