Why does Bernadette work at the Cheesecake Factory?

It is never explained that I know of. But Pasadena is in the middle of an area with several top notch universities (A couple of UCs, USC, loads of CSUs and of course CalTech) so there must've been loads of graduate students and perhaps not that many appropriate lab jobs.

In addition to the other answers, it's also worth pointing out that she only worked at the Cheesecake Factory until the Season 4 finale. Per the Wikipedia:

Bernadette worked at the Cheesecake Factory with Penny to pay off her debts in graduate school, studying to become a microbiologist. She met Howard at work as Penny introduced the couple. In the present, Bernadette has received her Ph.D, and was offered a job at a big pharmaceutical company named Zangen. Although her exact income is never specified, it is stated that she makes very good money (a "butt load") at a pharmaceutical company and that it greatly exceeds Howard's income.

I don't think her choice of work environment is that unusual. Bringing a little bit of my own personal life into this answer, I've dated two different women who were in the process of completing PHDs. Whilst one eventually worked in an academic environment towards the end of her degree, for the majority of their courses both worked in restaurants/cafes/retail.

Why? It was easy money and much more importantly it wasn't academically stressful, leaving them time to think, plan and even work on their PHD work whilst at their second jobs.

Well the writers needed Bernadette to meet Howard somehow. If Penny was to set them up, Penny and Bernadette needed to know each other. Hence, she works at the Cheesecake Factory.