The physical place is a mountain 山 やま
The NAME of the place you use 山 さん。
Thus ふじさん is a やま。
This works for all mountains in Japan
I just did an (intended-to-be-humorous) breakdown just above of mountains in Japan showing this is not the case, if you’re interested.
I know @Leebo already rebutted this, but I question with complete sincerity:
How do you explain 火山 (かざん)? Honorifics are never subject to rendaku, so how are we respecting the the volcanoes? That logic would also assume we would use ひ as the reading, since 火 (か) is not a word, so it would be ひさん.
You don’t have the level for this either, but 山脈 is also broken by this logic. Honorifics are also not usually placed at the beginning of words, so why is 山脈 さんみゃく and not やまみゃく?
ふじさん is correct
Attention mountain lovers, go watch
to get all this mountain-loving, and mountain-naming-loving out of your systems. It should also let you feel cool during a hot summer.
Mountains should definitely be respected (and they are in Japan) but that’s not why they’re (often) called –san.
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Is “oops I forgot” a sufficient answer?
Edit: I hope that after this topic is resolved it will be buried deep within the community, so my moment of stupidity will never resurface again.
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Hah, nooo. When it’s on the internet, it’s there forever.
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Yup, that’s fair! I originally that that the 「さん」from ふじさん was the honorific, too, when I first heard it said in anime. Before I started WK, my 訓読み were tremendously strong than my 音読み, so knew 山 was やま and assumed the Japanese were just being respectful to the natural wonder. That realization made me question all the the honorific-like words I knew like 逆さま, 奥さん, etc. to figure out which ones were honorifics and which were readings I didn’t know/kanji now replaced by hiragana. 
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Don’t tell anyone, but I confess I made the same error. Even posted about it in my travel blog, the day I climbed the mountain. That was almost eight years ago by now, though. 
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That’s why it’s a “rule of thumb” and not a “rule,” right?
Personally, I find it much easier to know the rule of thumb and then memorize the exceptions, rather than memorize every word individually. If the rule applies more than half the time, you come out ahead.
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that makes me feel better
It doesn’t seem like anyone’s mentioned it yet, but I’m sure I’ve heard people also refer to it as Fujiyama. I’m not sure if it’s a case of Western explorers historically misreading the kanji like with gingko, or if it’s an older / alternate reading. ふじのやま is an older name for the mountain, so it could come from that. Sometimes words have a different reading in different contexts. For instance, if 富士山 is referring to the battleship it’s definitely read as ふじやま.
Jisho lists ふじやま as a possible alternate reading for 富士山. I wouldn’t take that as proof of anything, but it means there’s at least some precedence for the reading, even if it’s just Japanese people historically misreading it themselves.
All that said, ふじさん is definitely the standard reading that should be learned. If you google ふじさん you get pictures of the mountain, if you google ふじやま you mostly get pictures of the roller-coaster. I just wanted to point out it’s not as clear cut as some people are making it seem.
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When you consider how common some of the words I mentioned are, I’m really not sure it would be over 50% for a beginner. (Talking about word usage incidence, not merely the percentage of kanji that fit the rule)
But no one ever mentions this and says “btw, newbies, this only helps 50.1% of the time”.
Obviously I’m exaggerating the number, but seriously, when people tell this to newbies here it’s often said with the conviction that gives the impression exceptions are actually rare.
It probably depends on whether or not the percentages are weighted by frequency. A lot of common words have exceptional readings, making the “rule” less useful if weighted by frequency.
I’m sure somebody could do an analysis of the words on WaniKani using APIv2 if they wanted…
I’m not sure usage frequency matters, though, since you have to learn each word exactly once, no matter how often you use it. To that end, it’s probably better if the exceptions are weighted toward the more common words, since those get reinforced more often.
As a beginner, I have found it to be a very useful rule of thumb, and I’m glad somebody told me about it, even though it has a lot of exceptions.
I guess I just want to see people even acknowledge that there are exceptions. Of course, then someone says “there’s always exceptions!” But hey, there are degrees of exception-having.
Like, “する and くる are the only irregular verbs in Japanese” has few enough exceptions, which are relatively hard enough words, that you can go a long time without ever questioning that one. I bet many people quit before they have to conjugate something like おっしゃる or 問う.
But the kanji rules are full of exceptions from day 1!
I accept that my complaints are not grounded in anything meaningful.
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