How can Gulliver's Travels be considered an example of "proto-science fiction?"
Gulliver's Travels is first and foremost a satire on the "adventure voyage" genre of fiction that was popular at the time, specifically Robinson Crusoe, which Swift is rumored to have despised for its European superiority and rejection of foreign culture as meritorious. However, several aspects of the novel are similar to those of science-fiction, especially the archetypal journey of a regular person (human from Earth) to far-off lands (other planets), meeting with strange creatures (aliens) and returning home with his story, which is met with disbelief.
Gulliver's journey to lands where the people are tiny or enormous is just as fantastic as meeting squid aliens on Jupiter. He even meets what might be termed as proper aliens, literal inhuman creatures called Houyhnhnms that are horse-like in appearance but entirely intelligent. Swift overturns the Euro-centric protagonist of common fiction by having Gulliver realize how inferior human culture is to that of the Houyhnhnms; unlike much of the sci-fi that followed, Gulliver is never able to affect or dominate other cultures with his own, finding that they consider him practically a barbarian.
Possibly the most sci-fi-like aspect of the novel is Gulliver's voyage to Laputa, the floating island, populated by brilliant scientists who are constrained by their minds and can barely function in society.
The flying or floating island is exactly circular, its diameter 7837 yards, or about four miles and a half, and consequently contains ten thousand acres.
Upon placing the magnet erect, with its attracting end towards the earth, the island descends; but when the repelling extremity points downwards, the island mounts directly upwards.
(Swift, Gulliver's Travels, gutenberg.org)
The imagery of a floating island has become a classic trope of science-fiction, and appears in works as diverse as the Cities in Flight series by James Blish, to 2009's Avatar by James Cameron. The image may well have appeared for the first time in fiction here, putting legends and mythology aside. It is even likely that Jules Verne or H.G. Wells used it as inspiration, being the commonly-assumed forefathers of sci-fi; certainly, they would have read it during their lifetimes. Overall, the use of different lands instead of different planets is the most important similiarity; Swift had no otherwordly context to place his extraordinary cultures, and so placed them on unexplored areas of the Earth, something which is less believable in the present day.
The enlightenment spirit promoted the equality of men and gave rise to scientific inquiry, which grew out of the 17th century rationalism. All of the 18th century philosophers saw themselves as continuing the work of the great 17th century pioneers- descartes, lebnitz, Newton and Locke- who had developed methods of rationality and empirical inquiry and had demonstrated the possibility of a world re-made by the application of knowledge for human benefit.
In voyage to Laputa many critics feel that Swift was satirising the strange experiments of the scientists of the royal society. The Laputians excel at theoretical mathematics but they can't build houses where the walls are straight and the corners are square. Instead, they constantly worry about when the sun will burn out and whether a comet will collide with the earth. This misuse of reason is hilariously elaborated on in chapter five and six where the various experiments occurring at the Grand Academy of Lagado are described. The Laputians, we are told, expresstheir ideas perpetually in lines and figures. Thus we can notice that Swift was depicting a society which believed that science could reveal nature as it truly was and showed how it could be controlled and manipulated. 18th century people believed that the human race would naturally use it's scientific knowledge to do good.