Learn Spanish (Latin America): El día es bonito.

You are right that most words ending in 'a' are feminine, but día (day) is one of the most common exceptions. It is actually a masculine noun, so it always uses masculine words like el.

Since día ends with an 'a', shouldn't the adjective be bonita?

Adjectives must match the actual gender of the noun, not just how the noun is spelled. Because día is masculine, the adjective must also be in its masculine form: bonito.

Why do we use es instead of está here? Isn't a beautiful day a temporary condition?

This is a common mix-up! We use es (from the verb ser) because we are describing the inherent characteristics of the day itself. We are describing what kind of day it is, rather than pointing out a temporary state or location.

Why does día have an accent mark on the 'i'?

The accent mark breaks the vowels into two separate syllables: DÍ-a. It also tells you to put the strong spoken stress on the 'i'. Without it, the two letters would blend into one quick syllable.