West Berlin makes sense as long as they don't push it too far. The thing is Cuba has little to offer anyone except some good tobacco. Nobody is going to start a big war over the loss of their tobacco supply.
Cuba has more the offer the Soviets than West Berlin does to NATO. People/countries pick their spots to make a stand and often symbolism or prestige matter than practicality.
But as of 1961, the Soviets havent lent the Cubans any credibility so they are likely to let it go.