Here's part of the problem as I see it (and have experienced).
Some people (who don't know computers) will react that way to anyone who does not have
a storefront. You may know your stuff better, but without a business license behind your name
you come across as yet another guy from the street who says he knows computers.
Does your roomates father know you? If no, then how would it sound to him that his son's
roomate offered to sell them a computer built from "spare parts"? Regardless of the quality
of the parts, that offer probably came across with as much appeal as offering to sell him
a car built from spare parts. He (the father) comes from a generation that still depends
on B&M being the standard of doing business (He may also have the mentality that
still thinks of computers as a more expensive device (as a whole) and is not prepared
to part it down to determine the cost over MSRP).
If you had built a system for your roomate instead, and anything (any little thing) had not
worked as expected, he (the roomie) would have never heard the end of it from his father.
Its not your fault his father did not shop around, but it would have been your fault for not
allowing them to go to a "reputable" establishment for their needs.
What helps people like that is not ridicule or offering to do the job for them, but education.
You should have sat down with the roomie and worked out type of computer (and parts)
he should be looking for, something that he could take to his father and show what
the state of the art is (or at least what is good for a mid-range computer). Something
he could have whipped out and run a quick comparision against while in the store looking
at the "student special".
Some people (most people) don't want to think about it, they just want someone to tell
them "this is a good deal", "this is a good price", and let them get on with the parts of their
life that are important to them. If you can't get those people to at least stop for a minute
and compare prices, its not your fault that they don't get a good deal.
A question though, did you see the receipt your roomate got for the system? How does
this builders prices compare to other builders in your area (not the big stores)?
Offer what help you can to help your roomate get the most out of that system, but
be careful you don't turn into his personal tech support over it... Explain everything
to him, even if you think he should already understand that stuff, so he can learn
to do his own upgrades and repairs, and may learn better how to shop for
computer stuff.