Is it the Altmer and their homeland I general, or is it the Thalmor?

Neither. It is a symbol of the Aldmeri Dominion.

And before that, most likely a symbol of Auriel.

Yeah, definitely leaning towards a symbol of Auriel.

It's not definitively the symbol of Auriel, but more the Altmer of Summerset Isles used an eagle as their symbol but not the one we see from the front with the wings spread outward and upward. Since the concept of the AD came from the Altmer, an Eagle is used and it really stems from their connection to the Aedra (and indirectly to Auriel).

The Eagle represents Auri-El, the head of the Altmeri pantheon. Just a fun fact, Alessia created Akatosh who is Auri-El(Eagle/Bird) + Lorkhan(Snake)= Akatosh(Dragon).

So would you say the glass and elven armors in this game represent the aldmeri dominion and auri-el, or do you think they represent the thalmor?

I would go as far to say as none of those things. The particular style of the Elven and Glass armors in Skyrim, represent the Altmer's view of style. Elegant yet durable, light yet very protective. The Altmer consider themselves the most superior race in Tamriel. Their style in armor is in a way reflecting that. They want to give the air of refinement yet intimidation. Which is a stark contrast to the rugged look of Man made armors.

At this point, anything that represents the Thalmor likely represents the Dominion as well (and vice versa).

So Noble, what you are saying is that Altmer as a race and society, strive to create rich, ornate and effective armors, regardless of being a thalmor or not.

And stred your saying that if I wore the armor I would representing the thalmor regardless of who I play?

Exactly. http://www.imperial-library.info/content/arms-and-armor-altmeri-champion-falandamil.

Also the Altmer are known for their artisans. Some artisans are also blacksmiths, and they combine those two respective skills, to create arms and armor that are known for their artistic inspiration and highly efficient quality; in both protection and offensive capabilities.

OK. So lore wise, to be an altmer who is NOT a thalmor or thalmor supporter, using glass armor would be OK.

Yeah of course. You also have to take into to account that more than likely, a lot of Altmer in Alinor right now, probably do not like the Thalmor anyway. Up until 4E 20, the Thalmor were a very minor political faction, the only reason they gained power was in response the widespread destruction of the Oblivion Crisis and the destruction of The-Crystal-Like-Law, which all of Summerset Isles was very saddened over, and this weak state of the Isles was the perfect time for the Thalmor to take advantage of the huge fallout and hence you have the Third Reich Old Mary.

What the races of Men see in a flaming dragon (Akatosh), the races of Elves see in a gleaming golden eagle (Auri-el).

Like how the swastika was forever tainted by the Nazis, the Thalmor have co-opted the golden eagle's symbolism and have tainted its meaning with their malignance.

Though Auri-El is pre-Convention and Akatosh is post-Convention Alessian view on time; as I said before Auri-El(Eagle/Bird) + Lorkhan(Snake)= Akatosh(Dragon).