if you go for deals on manufacturer PCs, and are smart about it, you can never build a computer that price matches, the Windows Premium is often too much to handle.
however, the biggest advantage to building a PC instead is component balance, if someone wants to buy a PC to game, he can easily build an entry level one for 500 bucks like logainofhades and alloco91, while PC manufacturers will often go into the 700/800 range before even offering discrete GPU options.
if you just want a computer for work/productivity, you can easily find a coupon online and get a high end i5/low end i7 computer for about 500 bucks, which is literally impossible to beat for a self builder.
in summary, building your own gives flexibility and allows you to balance the components to your desires, which is VERY important for people looking to game.
Anything PC wise is expensive if you don't know what you're doing, as long as you are a smart buyer nothing is really all that expensive