If you are interested in the early history of football, I would highly recommend you check out "The Big Scrum: How Teddy Roosevelt Saved Football" by John Miller. Its a nice, quick read and looks at the early history of the game and its development up though the early 20th century and the introduction of the forward pass, principally concentrating on the press for reform of the game that came about in 1905, of which President Roosevelt was one of the most vocal supporters. It covers how scoring evolved in those days, and other changes to the rules.

Edit: I started with my source and forgot to actually give you the answer... As the book will detail to you, there have been quite a lot. In the very early days, there was no standardization, and the game was played by the host's rules - the first Harvard-Yale game had Touchdowns worth no points, simply earning you a try at kicking a goal after for a single point (you could also chose to kick from the field during play). The first standardization (due in large part to the efforts of Walter Camp), in 1883 was two points for a TD, kicking a goal after the TD was worth four points, and kicking a goal from the field during play was worth five (that is to say... a field goal!). A safety was worth only one point. A year later they tweaked it, switching the Touchdown and the following kick for four and two, respectively, and making a safety worth two. You still got five for kicking a field goal.

A few more changes happened, and we would end up with the current scoring scheme in 1912, with the only change since being the addition of a two-point conversion in the 1980s.