My theory on this is it's actually was a city built by both Dwemer and Snow Elves. Firstly it has no Falmer in it, secondly the entrance to Blackreach is in the Cathedral.

You have to ask if Dwemer are not known for being religious then why have something generally considered religious, which is why my theory here seems most sound, and probably why Falmer stay out, out of respect of their past.

I like your theory, but the Dwemer constructs will actually forget about our characters to kill Falmer. The only Dwemer Ruin above Blackreach that does not have a lift or access to Blackreach does have a Falmer statue though.

A little bump as I wish to see others thoughts on this.

This is a good question. Although I have no answers, it is worth suggesting that perhaps the Dwemer were/are more religious than we originally thought?

Its called a Cathedral by the game, but that doesn't mean that was what the Dwemer called it. Could just be a lecture hall.

That seems rather flimsy reasoning, since most places keep their original names.

Yes, Alot of the names of the areas in Dwemer ruins seemed to be names given by post-dwemer races. An example can be during the College of Winterhold quest in which you go into a dwemer ruin, you meet a mage at the end, I think he's given the name of the room "Oculory" As he says " I don't know what the dwemer called this place, probobly something unpronunceable".

Again that only the explored ruins, but the ones not explored, the names remain same...

I wouldn't say so, most of the dwemer ruins have been explored before your character even gets there, after all they've been there a long time. Mjoll explored Mzinschaleft, From-Deepest-Fathoms explored the dwemer ruin assosioated with her quest.

Well consider that other names remain the same, why? My idea is the only one that doesn't have any holes.

No proof either

A Cathedral is considered something holy, thus why give the name of some location in a Dwemer Ruin this. That makes no sense.

Because it reminded the developer who named it of a cathedral?

@Amazon, cheap reasoning is cheap, the whole game meant to be immersive, thus something like that wouldn't be allowed.

Maybe your theory is right, but its just a theory lacking evidence to support it.
In the meantime the developers had to call it something in English.

Is it possible that the Falmer "Servants" use it for some kind of worship and that maybe they renamed it? I haven't been to Blackreach in a while so I'm not completely sure of it's proximity to where the humans are allowed to go. Of course, if they renamed it how would the topside world know and why would they care?

Last point is exactly what I mean!

The name of the initial Dwemer City/Structure stays the same, but not the different sections.

Now I'm gonna' have to check it out again and look around.

I viewed that as not meaning a religious cathedral. But rather a grand room in honor of their technology.

More like the third definition in:

http://www.thefreedictionary.com/cathedral

This.

After going back and thoroughly roaming around and looking at the overhead map view from several locations inside it definitely resembles a cathedral in layout (aisles (crude pathways on either side), transepts, and an apse (the elevator). It even has a basin in the entrance that looks like a font (holy water 'birdbath'-like container). The mechanism that grants access to Blackreach is even positioned as an altar (location and architecture) - if an explorer without an Attunement Sphere came upon it they may assume it was an altar (I didn't know WTF the mechanism was the first time I saw it on my first character and I think I assumed it was some kind of altar myself. ).

FWIW: there were Falmer (low level Falmer) in there, but I don't recall if they were in there the first time I cleared it.

Edited for content.

The Cathedral is the point where the Dwemer first found the Drained Magma Dome that is Blackreach, if you listen to Septimus' rantings he does say "Alfthand, first point of puncture".

But I believe that Alftand is explored by humans. In Blackreach, there is an alchemist's laboratory, and since all elevators to Blackreach are blocked I think he had to pass through what is now called the Alftand Cathedral. Besides, the Dwemer didn't have to call it a cathedral, as long as the people who discovered it called it that. You have to admit, it does look like a cathedral. And in one of the loading screens, it is mentioned that the Dwemer pray to their gods of Reason and Logic, meaning that the cathedral may after all be there for religious reasons.

Short recap:
1. Alftand probably has been discovered before.
2. Maybe the Dwemer didn't call it a cathedral, but the people who discovered it did.
3. The Dwemer did have their gods, so it might be a cathedral after all.

I hope this makes sense.

Falmers did build the giant statue of the falmer in one of the ruins, so it's entirely possible that some structures were built by or were built for the falmers.

And what better place than a lecture hall to worship Logic and Reason, and engage in enlightened Debate?