Hi @Antani
If you search the forum you'll find several threads on this. The reason why so many taxa are only being classified as Fungi is because there are no outgroups in your reference set. That is, these sequences are likely non-fungal eukaryotes see, here, here, and here.
This issue crops up with other reference databases too, like rRNA reference sequences.
I recommend using the unite database that also contains non-fungal eukaryotes.
-Mike