I think there's something Grizzly (and many of the subsequent posters) could benefit from remembering. There are A LOT of dudes left out in the bread line looking in at Naval Aviation. You're going to fly Super Hornets and not Growlers. To use a tired cliche - first world problems.
My reluctance to support the "go ask why" plan is formed from seeing it done EXTREMELY poorly on several occasions, not just out of the VTs, but also from the RAG. You're likely going to ask the question of someone (someones) who at some point didn't get their first choice, and may have little appetite for your inquiry. Some of the guys you may be taking this question to likely had eight options when they left flight school (VF, VFA, VS, VAQ) and may have gotten their fifth or eight choice...
John offers a glimmer of hope that you could identify a scoring error - but I offer that chance is WAY over in the by-exception category and not the rule.
IF you decide to pursue that course of action I would encourage you to do it as graciously as possible and to remember that it's a pretty common practice for VT IPs to call their boys at the various RAGs to give an unofficial read in on an inbound Cone - and it's not usually to tell them how awesome he is. One of the most commonly used conduits for this is from VT to RAG Paddles.
Another factor that may be at play; the days of VAQ (G) getting nothing but first round draft picks is over. Has been for some time. The spread between 106 (C/E/F), 122 (C/E/F), and 129 is much more equitable and qualitatively spread than it had been for 129's G infancy. As far as you know 129 may have taken three first round draft picks in a row and 106 was due.
Again, if you decide to pursue, I encourage you do to it with caution and humility. This WILL NOT be the last time you don't get what you want in your career and there is not an appeal or inquiry process at each step of the game.