Why is it a pair of pants when it is one garment?

The phrase is a fossil of how the garment used to be made. In earlier European clothing, leg coverings were often two separate items, one per leg, each tied or fastened to a waistband or doublet, so a pair of hose or a pair of breeches described exactly what it was, two pieces. When tailoring joined them into a single garment, the naming convention stuck, and English kept describing the item as a pair long after it stopped being one.

English does this with a whole class of two-part objects, which is why a pair of scissors, a pair of glasses, a pair of pliers, and a pair of tweezers all refer to single tools with two symmetrical halves. Linguists call these pluralia tantum, nouns that appear only in plural form, and they take plural verbs, my pants are, not my pants is. The related trivia: pants comes from pantaloons, itself from Pantalone, a stock character in Italian commedia dell'arte known for tight-fitting leg wear, and the word means underwear rather than trousers in British English, which produces reliable transatlantic confusion. Trousers, meanwhile, took its plural form by analogy with the same pattern.