No, pacifiers don't always work.
Using the pacifier too many times when the baby clearly doesn't want it and you will actually increase the crying.
It's usually obvious when the baby doesn't want the pacifier. The baby will open his mouth to drop the pacifier. The baby will wriggle his head out of the way of the pacifier when you try to give it to him a second time. The baby will cry like it's about to be murdered when it sees the pacifier (this will usually happen on your third or fourth attempt). And in some cases if the baby has enough dexterity, the baby may even take out the pacifier and throw it on the floor, and then give you an evil stare -- all the while continuing to cry its little lungs out .
Usually, a mother will know what's bothering the baby depending on the actual cry of the baby. If the mother doesn't know, she can just try different things until the baby stops crying, or until the baby cries itself to sleep.
In the case of an airplane, the crying is usually triggered by the change in pressure which causes pain to the baby. And here is the official advice given for that:
But even implementing that advice (which includes using a pacifier and other tips) from the second page doesn't guarantee that it will always work.