Are there fungi that are directly beneficial for humans?
Saccharomyces boulardii.

https://en.wikipedia.org/wiki/Saccharomyces_boulardii

S. boulardii is a yeast, closely related to S.cerevesiae (if not the same organism).  There is a lot of solid data showing use of this fungus as a probiotic can help treat or prevent intestinal infections.  

Systematic review with meta-analysis: Saccharomyces boulardii in the prevention of antibiotic-associated diarrhoea.


  RESULTS:  Twenty-one randomised controlled trials (4780 participants),
  among which 16 were new trials, met the inclusion criteria for this
  updated systematic review. Administration of S. boulardii compared
  with placebo or no treatment reduced the risk of antibiotic-associated
  diarrhoea (as defined by the study investigators) in patients treated
  with antibiotics from 18.7% to 8.5% (risk ratio, RR: 0.47; 95% CI:
  0.38-0.57, number needed to treat, NNT: 10; 95% CI: 9-13). In children, S. boulardii reduced the risk from 20.9% to 8.8% (6
  randomised controlled trials, n=1653, RR: 0.43, 95% CI: 0.3-0.6); in
  adults, from 17.4% to 8.2% (15 randomised controlled trials, n=3114,
  RR: 0.49, 95% CI: 0.38-0.63). Moreover, S. boulardii reduced the risk
  of Clostridium difficile-associated diarrhoea