That's actually the nice thing about it. After you've designed and debugged your project on the Arduino board, you can implement it with a $2.50 AVR (+ a few support items).
You can't do that with, for example, the Raspberry PI or the Netduino.
That makes sense, but what doesn't is incredible amount of projects and things (and not only DIY, I've seen some one of commercial designs done exactly in this way) that just embeds whole arduino board connected by bunch of random wires to something (preferably something composed of another relatively expensive breakout boards).
For one-off projects, the 25 extra bucks aren't really the killer. I don't see the problem with using an arduino in a commercial setting, so long as you're not mass-producing with said arduino.
