I thought so too, but at the time I was just thinking that I wanted her to win...that was my only reasoning. I didn't care about Neji's skills or anything else. I was like 11 or 12 at the time where my logic= Hinata is good, Neji is bad, Good always beats bad, therefore Hinata should've beat Neji.
Knowing what I know now, it all makes sense that Neji should win. If you're still at the chuunin exams, I recommend that you catch up really quickly. Epic things are going to happen!