How to deal with poor teaching evaluations on academic job market?

Everyone has a tough time the first several years of teaching. It takes several years for people to find their feet. We can't all be Richard Feynman right out of grad school.

Still, a search committee might note your poor scores. You can compensate in several ways:

1. By remarking on this in your Statement of Teaching. I would try not to dismiss or shift blame, but tackle it head on. "In my first year of teaching, I received poor scores in Nuclear Physics 101. These mainly centered around X and Y. I have revised my syllabus to handle X and will dedicate more time to discussion around points Y. I have also changed how I handle Z, which should alleviate both problems, etc. etc. I have also decided to be less of a jerk."

2. By delivering a stellar guest lecture when you're brought on campus for your interviews.

Note that #1 and #2 both involve practices (statement of teaching; guest lecture in a class) that not all universities and colleges follow. Generally the ones that care about teaching require them and the ones that don't don't.

For example, I teach at an R1 where undergraduate teaching is ... deprecated. We mainly care about your research and that's what we evaluate our candidates on.