This carbon dioxide is not put into the bottle by humans. Cider, for example, is filled with carbon dioxide along with sweet water, but the carbon dioxide in beer is a natural product of the beer making process.
Beer is made mainly from barley, yeast for fermentation, and hops for flavor. The yeast converts the sugar contained in the barley into alcohol, which is then used to make beer. During this process, carbon dioxide is released from the yeast.
This carbon dioxide is kept from escaping and is contained in the bottle, resulting in the formation of bubbles. In addition, the protein in the barley and the ruburon in the hops keep the bubbles from disappearing, so unlike cider, the bubbles in beer do not disappear easily.