The differences between John Locke and Jean Jacques Rousseau have to do as much with attitudes as with systems. Both advocated political liberalism and religious tolerance, but their conceptions of human nature differed.
Locke believed that humans began as tabula rasa (erased tablets) and gradually acquired knowledge through experience. Education was an important civilizing force for him. Society depended on a social contract, in which we agree to behave well to each other reciprocally in order to create preconditions for good lives (i.e. if everyone agrees not to murder and steal, we can devote our time to things other than self-defence). Locke admires reason, sees social and political order as ideally founded on reason and reciprocity, and sees civilization as admirable.
Rousseau thinks that humans are innately good and that civilization and traditional schooling are corrupting influences. He sees emotions and sentiments as more important that Locke does.
While both John Locke and Jacques Rousseau believed that every individual should be free and that no one should have to give up his/her natural rights to a king, both differed on what this state of affairs should look like. Locke believed in limited, representative government but Rousseau believed in direct government by the people.
Locke believed that the powers of a king or government were to be limited in scope. He believed that a ruler or government should exist only to protect life, liberty and property, and if the government overstepped its authority to the point of totalitarianism, the people would have the right to overthrow such a government. This unique idea of freedom was apparent in his seminal 1690 work, entitled "Two Treatises Of Government." It's important to note that Thomas Jefferson paid homage to this revolutionary idea of the right of the people to overthrow an unjust government when he wrote the Declaration of Independence for the United States of America. Unlike Hobbes, who favored an absolute monarchy ("absolutism"), Locke favored representative government, with power held by the House of Lords and the House of Commons. Along with separation of powers, Locke's ideas greatly inspired the American form of government where power is vested in a bicameral legislature, along with the executive and judicial branches. All three were to be checks on each other's powers. Locke's "Two Treatises" defended the tradition of the ancient law of the Jews, which stipulated that no ruler was free to do whatever he wanted because there were moral laws which encompassed all.
Rousseau, on the other hand, was extremely adamant in his belief that man "is born free and everywhere he is in chains" (opening line of his political treatise, "The Social Contract"). He believed that it was society that corrupted the nobleness of man. Rousseau defended the right of the people to rule, and he insisted that the people were accountable only to the people themselves and that no ruler had any right to subjugate the will of the populace. He believed that all should have a vote in political affairs and that the majority vote should decide the general will and direction of any country. The words "We the people..." at the beginning of the Declaration of Independence were directly influenced by Rousseau's belief in the wisdom of the people to decide their own course of affairs. Rousseau also believed in separation of church and state, a belief that has encapsulated much of American government.