You appear to be well qualified. The main sticking point would seem to be your relatively low amount of cross-country time. As John Burke noted, a company's hiring decisions can seem mysterious and sometimes there's no good reason why a qualified applicant gets turned down. Don't take it personally. There's a couple of ways to proceed from here:

(1) If you like your current job, stay there and reapply to Skywest again in a few months. This might also be a good time to consider where else you might want to work if Skywest isn't interested in hiring you. Apply everywhere you meet the minimums.

(2) If you want to build up your IFR and cross-country experience, consider working for a Part 135 operation for 6-12 months. I found that my Part 135 experience was great preparation for my later airline flying. It's never been a better time to get hired at an airline, but training is still challenging and will require a 100% effort. Every bit of instrument, cross-country, and multiengine experience will help.

Good luck.