The Pontiac Aztek has something of a reputation. A bad one. It was Pontiac's failed attempt at making a crossover model: a midway model between a minivan, a pickup truck, and a full SUV. The public hated it, and it sold poorly. To add insult to injury, it consistently finds itself included in lists of the world's ugliest cars.
So it was the perfect car to symbolize Walt's own situation. An unappreciated genius, who is stuck doing a thankless job, working with kids who couldn't care less about his passion, and struggling with paying the bills. He is tired, demoralized, and too mired in his own self pity to do anything about it. To symbolize this even further, the Aztek was painted a washed out shade of beige (that was never an option in the actual Azteks).
When Walt finally comes into his own in season 5, and becomes his own man, more assertive and aggressive, he ditches the Aztek for a sleeker and sexier Chrysler 300. His transformation into a drug lord complete.