I can see what Chris is getting at, as many common names are fairly similar, but relate to fungi from different genera, and sometimes the common names could imply that they might be related.
I agree with Rob though, that for all but the academic, beginners to fungi will no doubt "discover" the common names far more readily than they will the Latin names.
I don't particularly think there is any real problem here, since most people will only ever have a passing interest, so common names will always be the "norm". - When did you last have a conversation with a neighbour or friend where they recalled a day's outing to the countryside with Latin names for everything they had seen?
I still very much count myself as a fungi beginner, but with perhaps a little more interest than most folk, and it now seems natural to want to know the Latin names. (Which in a lot of cases I now remember when I can't remember the common names).
What I see as more of a problem to the person who does take the interest a little further, is the amount of conflicting information contained within readily available literature etc.
For example, I recently found Yellow Stainer -
Agaricus xanthodermus.
Phillips says "Occasional, vulnerable on Red Data List". (I thought I had found something special). However: -
Jordan says "frequent".
Sterry/Hughes say "Widespread & common. Probably the most common
Agaricus species".
Another example - Olive Oysterling -
Panellus serotinus: -
Phillips says "Frequent".
Jordan says "Infrequent or rare".
Sterry/Hughes say "Frequent in England".
I now know that cross checking with FRDBI or Index Fungorum gives a truer picture, but you would think that there wouldn't be directly opposing information in what are generally recommended as the best of the non specialist field guides.
Ah well, it all adds to the fun I suppose

Regards,
Mike.