Besides the performance aspects already mentioned by the other replies here, there's also a safety issue.
The database's catalog views (that keep track of the tables, columns, permissions and all that system stuff) are always located in the primary data file and you can't change that.
If you can separate out that system catalog data in the primary data file, and put your user data into a secondary file, the primary file is smaller, gets a lot less updates and inserts, and thus the chance of corruption by e.g. a bad disk sector is minimized.
If your system catalog views (and their underlying tables) are damaged or destroyed, your entire database will be toast - so you definitely want to have the least chance of damaging that primary data file.
That's probably not a big issue in a smaller to medium size database, but might be a point to consider in a larger setup.