OK, it's not a subway. At all. But it is a train. (With a snack car!) And from Atwater Village it's a painless walk to the Amtrak station in Glendale.
At the other end, in Ventura, the tracks are one block from the sand. Travel time: 97 minutes.
A train to the beach in Santa Monica could take 10 years longer. And cost $4,799,999,983 more.
To get zen about it, don't change how you go to the beach in Santa Monica. Go to the beach in Ventura County.