Simply due to the nature of the position, first basemen will record many more putouts than a third baseman, but the opposite may be true for assists. Fielding percentages uses both of these statistics, along with errors, to gives us a general idea of good a fielder is.
To figure out fielding percentage, we take Putouts + Assists and divide it by Putouts + Assists + Errors. Sometimes you will hear this later part called total chances.
Now, each position can be compared more accurately—although fielders with a high fielding percentage and a large number of total chances will obviously standout.