At first having the old man around was a boon to Elisenda and her husband. They had become very rich from selling tickets for people to see the "angel." As the weeks go on, however, the old man becomes a nuisance to her. He is no longer a curiosity, and everybody in town who wanted to see him has already done so. There is a new show in town--the spider woman. Besides the loss of money, the old man seems to be following her and to be constantly in her way. When he finally flies away, Elisenda is relieved for both of them--for herself because she'll no longer have this annoyance; for him because they were worried that he might die and because maybe she feels some sympathy for the poor old man who might now return to his home.
The answer to your question is given in the last sentence: "he was no longer an annoyance in her life but an imaginary dot on the horizon of the sea."