Estragon and Vladimir are both lonely characters whose loneliness is enhanced by their inability to truly understand each other. They wait together on the road for Godot, not sure what day it is or if he will ever come.
Though caught together in a state of stasis, the men don't truly hear what each other has to say. Estragon is absorbed in practical and immediate problems, such as getting his boots off or his hurting foot, while Vladimir is preoccupied with the bigger philosophical problems of humankind. Rather than sympathize with Estragon's pain, Vladimir scolds him for using his boots as an excuse not to deal with larger problems.
Although the two are lonely and alienated from each other, their desperate desire for some company leads them to stick together and lose their individuality. For example, while they contemplate suicide as a way out of their lostness and even find a tree limb to hang themselves on, they fear doing it. Their fear is that Estragon will succeed and break the branch, leaving Vladimir alive and all alone. They both would rather stick waiting endlessly on a road in the middle of nowhere, never completing their journey or taking a meaningful independent action, to being entirely alone.
This loneliness leads to submerging one's individuality in an alienating and inadequate relationship with another human being rather than ending up completely isolated. This acts as a metaphor for the human experience.