Innate skill and experience, but mostly experience. As with most things the more you do, and the greater the variety, the better you get (probably).

It's largely to do with building up tool sets. As you become more experienced you have more past solutions (experience / tools) that you can bring to bear on the current problem and better understanding of the different trade offs each possible solution may entail.

Since you have already discovered PerlMonks you are already in a good position to gain useful experience: delve into the Seekers of Perl Wisdom archives and try your hand at solving the various problems presented there. When you feel confident, contribute answers of your own to current questions. This is an excellent place to gain experience at almost any level!