Correction: Arduino is a set of libraries, an IDE, and an MCU together. It is not "a form of C", it's just a bunch of C++ libraries - it leverages avr-g++ to do the compilation. Learning C/C++, by the way, will go a long way in this kind of thing.
Both the Arduino and the $50.00 robot tutorial use AVR microcontrollers (Arduino has ATMega328, $50.00 is ATMega8, ATMega168, or ATMega328). The advantage of the Arduino is simplicity - you don't need to learn much. The advantage of the $50.00 robot is complexity - you will learn a lot more.
Theoretically, you could just combine them - flash the ATMega on the $50.00 robot board with the Arduino bootloader, and add a $.50 16mhz ceramic resonator.
The program download doesn't work because it's for Windows. Simplest thing on *nix systems is to use the command line, and calling avrdude directly. Short of that, use Eclipse and the AVR plugin. Both of these are more complex - you may want to start on a windows computer.
You can use Arduino's IDE on Mac OS X: this could be an advantage for you. Once you've worked out these basic problems, come back, and we can help you with the code.