Originally the Fey used these markings as a sign of wealth, with the shape and coloring of the markings coming down to personal taste. Fey of high standing with vast amounts of resources available to them started to decorate their faces with dye to help them stand out.
Dye, especially brightly colored dye, was expensive. Also, painting a design and making sure that design didn’t alter from one day to the next was seen as time consuming, tedious, and something that requires a delicate hand to get right. Painted markings were meant to show that the wearer had extra resources to spend on dye as well as someone trained and available, day after day, to paint them on.
Thanks to the renewed interaction with the mortal world, the Fey have gained access to things like makeup, stencils, and cheap dyes. As a result, facial markings have become a bit of a fad over the last forty years or so. Now a number of Fey from all ranks and economic standing are sporting facial paint.
Some of this is just for the sake of the fad and fashion, but for other Fey the markings have begun to take on meanings not originally intended.
Some have started using these fur markings to show allegiance to each other - through families and guilds.
There are a few who believe the markings have protective powers, though this has never really been proven. Stones, amulets, and jewelry are considered by most Fey to be more reliable for invoking protection, or the occasional love spell.
Others believe the markings themselves will actually bring wealth. This also has never been proven.
While painted on markings are the higher status version, permanent magically created markings are used by some Fey. Many Fey that are powerful shape-shifters, like Puck, have chosen permanent markings so anyone familiar with them can tell at a glance who they likely are, even if their form has been altered.
Some Fey will also permanently mark others who they consider "theirs" with designs similar to their own painted on ones. This can be a problem if the Fey decides they no longer want control of the person, since magically made marks won’t come off, even with magic.
The facial marking fad is still considered new by Fey standards, so many still choose to not decorate their faces with symbols. This may change over the next few hundred years or so.