What are my chances getting into UC's and CSU's?

[Corbett]

Im aethiest, will pepperdine count that against me because they listed under really important religious affiliations etc

Pepperdine has a supplemental question on the Common App that reads as follows:

2. Pepperdine is a Christian university committed to the highest standards of academic excellence and Christian values, where students are strengthened for lives of purpose, service, and leadership. Students, faculty, and staff members of all faith traditions are welcome to become part of the Pepperdine University community. How has faith influenced your life thus far and what will you add to the continued conversation of faith on campus? (50-300 words)
   First-Year Applicants | Pepperdine University | Seaver College

If you are an atheist, it may be unusually difficult to come up with a compelling answer to this question. You might have to get pretty creative.

Note that even if you do get into Pepperdine as an atheist, you will still have to meet the requirements for attending religious services, which include 100+ sessions of chapel, bible study, etc. over four years. You will also have to take some religion classes, regardless of your atheism or your major:

Each semester, all undergraduates are required to attend 14 programs in the Convocation Series, which are activities aimed at building Christian faith, affirming Christian values, or addressing ethical and moral issues within a Christian worldview posed by current events. Most frequently, students attend the Wednesday morning chapels at Firestone Fieldhouse. Other programs include student-led worship services, small group Bible studies, and individual spiritual mentoring sessions with faculty or staff sponsors.

Additionally, all undergraduates are also required to take three religion courses as a graduation requirement: The History and Religion of Israel, The History and Religion of Early Christianity, and Christianity and Culture.
Chapel | Pepperdine University | Seaver College