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Right, you can over-write the arduino bootloader and use as bare chip. Only suggested the arduino because they are cheap and flexible with all their stacking boards. You did notice the bare bones kit can be plugged into a breadboard?
You can buy a breadboard adaptor from Sparkfun and solder some male pins to it. Or you can just make one from a chunk of double sided proto board. You then would have a setup **broken link removed**, and ready to program your AVR.
Hope that answered your question?
To the OP, use a USB programmer, regardless.
History has a way of repeating itself. AVR's, PIC's doesn't matter, neither are immune to RS232 port programmers working in a modern world. For instance, problems relating to the DIY JDM PIC programmer posts abound on the forum, works for some or most, others not. And yes it can be related to the user host device, and/or interface cable as you have mentioned. I would suggest to nip any frustration at the bud, by eliminating these variables.
If you're a beginner building your own programmer without knowing what you're doing is going to be nothing but added grief, simple programmers are very inexpensive and well worth the investment. Basic is a good language to start in, Swordfish basic is probably one of the more powerful one's out there but it's pay software. Basic would be a decent place to start as you can do many things with it, it will get you quick results, but at some point if you decide you want to develope anything serious you'll need to learn assembly and/or C