Learn French: Où est le musée ? Il est loin. - Where is the museum? It is far.

The grave accent on où (where) is only there to help you tell it apart in writing from the word ou (which means "or"). Both words are pronounced exactly the same way!

Doesn't the -ée ending on musée mean it should be feminine?

Normally, yes! Most French words ending in -ée are feminine. However, le musée (the museum) is a common exception that is masculine. That's why we use le instead of la.

Why does the second sentence say il est loin instead of using a word for "it"?

French doesn't have a neutral word for "it". Every noun is either masculine or feminine. Since le musée is masculine, you must use the masculine pronoun il (which means "he" or "it") to replace it in the second sentence.

Can I just use loin by itself to say "far"?

Yes! When you just want to say something is "far" in general, loin is all you need at the end of the sentence. If you wanted to say "far from" a specific place, you would need to add the word de (from) after it.