That's how Trek rolls, pardon the pun. I have the Madone 3.1 and they really give you crap bars, stem, wheels, tires, saddle, FD, chain, and brakes so they can fit a pretty nice carbon frame at a given price point. All of those things have been replaced with the exception of the Tiagra FD, which does its job. Clearly their marketing works, because in hindsight it'd be easier to pay upfront for the frame and components you actually want, rather than a complete bike and $400 or whatever over time to replace each part in sequence.

If you have those same non-name brand black brakes (Tektro? They were unlabeled on mine), be careful. The return spring rusted and stopped working on my front and rear calipers after about a year and a half, so the brakes turned to mush. Replaced them with SRAM Apex and it's been fine since.