I think you have a misconception about Darwin's role here. Darwin was not "telling them what to do." He was the "gentleman companion" of the captain, Robert FitzRoy, and was paying his way. They were going to all of those islands anyway, because the purpose of the ship was to do surveying and measurement. Darwin was there to both keep the captain company and amused, and to make natural philosophical observations. (In Darwin's mind, he was emulating his great hero, Alexander von Humboldt, but his scientific career was just beginning.)

Which is to say, Darwin was not running the show, nor was he doing anything that was not to be expected of his role on that kind of ship on that kind of voyage. He was not the only person on board doing such things; there was also an artist who was drawing and painting everything they saw as well, and people charged with taking the measurements (surveying, hydrographic sounding, etc.) that were at the center of the mission. You also have to remember that Darwin was not at all established at this point in his life; his work on the Beagle is what would make him a respected scientist. Darwin did make many observations but most of these were just in the course of the ship's normal activities. In some cases, like his collection of finches, he was not the only one doing it: the captain also fancied himself interested in natural philosophy and game, and led expeditions to shoot birds which Darwin participated in (and got to examine the fruits of the work). One should remember that in the case of the finches, it was not until he was back in England that their importance seemed clear to him — at the time, he was just cataloging whatever nature the ship seemed to encounter, which included birds because various members of the ship enjoyed hunting them for sport and food (in one famous case, he realized only while they were eating a bird that a crew member had shot — now called Darwin's rhea — was a species previously unknown to science).

As for what every member of the crew thought, obviously that's hard to know. FitzRoy reported in a private letter to another captain that "everyone respects and likes him," and claims that he took to sea life very amiably and quickly. FitzRoy recorded that one mate on board claimed that "I think he was the only man I ever knew against whom I never heard a word said; and as people when shut up in a ship for five years are apt to get cross with each other, that is saying a good deal." All of the reports that FitzRoy gave appear to relate to Darwin's interactions with the officers, not the regular crew. There are some indications that Darwin made at least one friend among the regular crew.

All that being said, five years is a long time to be amiable, and there was at least one point when FitzRoy was so angry with Darwin (because Darwin suggested that the abolition of slavery was the only moral opinion) that he asked him to leave. But he reversed his course a few hours later.

When one reads about the Beagle voyage, there are many instances in which the crew were quite unhappy — but these had to do with FitzRoy's choices. Darwin barely appears as an item on their radar compared to him — he was the one who was running the show, he was the one with the big personality and mercurial temper, and he was the one who made the kinds of decisions that would make them mad (like having the ship back-track at times).

Today we consider Darwin to be the central point of the expedition, but this is an after-the-fact judgment made because of his later fame and the later revelations he had into what he saw.

Desmond and Moore's Darwin contains several chapters on the Beagle voyages, and there is a volume known as the Beagle Record which compiles many of the letters, logs, drawings, and so on made on the ship.