Why didn't they call his first name Tom then?

Eye-rolling because they made it his first name and not his middle? It's a cultural phenomenon. There's no wrong or right in this.
I go by my middle name. So does my dad and one of my sisters. Who cares if he's Dovahkiin Thomas or Thomas Dovahkiin. I knew a guy whose first name was Royal, as in Royal John Doe. I knew another guy whose first name was Captain, as in Captain John Joe Doe. And how about this guy:
http://leatherhelmetblog.com/2010-articles/july/wonderful-terrific-monds-ii-name-champion.html
Don't prophesy this kid a bad future. His name means "dragonborn." That's pretty frikkin awesome. Be glad the couple didn't name their kid Mehrunes.