You need to understand that the California economy is built on agriculture. It and support services account for $100 billion dollars annually.
These inspections stations are used to ensure that potential pests that might decimate an entire crop are found and removed at the border. California's geography is such (mountains and deserts) that the agricultural heart of the state is protected from the NATURAL ingress of pests. Then came the humans, and transportation.
Between the medfly, the glassy-winged sharpshooter, and phyloxera California has lost BILLIONS of dollars in crops and remedial activity to address infestations.
No, we don't care about your pets, and we won't be stopping you on your way out.
Here's a description of the program if you want more information.
Here's the key snippet from this link:
About Our Stations
California’s Border Protection Stations (BPS) are the first line of defense in our pest exclusion efforts. At these stations, vehicles are inspected for commodities infested with invasive species. California established its first agricultural inspection stations in the early 1920s. Today there are 16 of these facilities located on the major highways entering the State (see interactive map below).
In 2008, more than 22.1 million private vehicles and 7.3 million commercial vehicles were inspected at the BPS. From these vehicles, inspectors rejected over 43,000 lots of plant material (fruits, vegetables, plants, etc.) because they were in violation of California or federal plant quarantine laws.
From these interceptions, inspectors found and submitted 9,314 specimens (i.e., insects, diseases, weeds, mollusks and vertebrate animals) to CDFA’s Plant Pest Diagnostics Lab for identification — over 2,500 of these specimens were exotic invasive species capable of causing serious damage. Among these were: Gypsy moth, Asian citrus psyllid, quagga mussel, imported fire ant, cherry fruit fly, Japanese beetle, spotted knapweed, cedar–apple rust, and glassy–winged sharpshooter (just to name a few).
One last thought: if you ever travel to Hawaii, you will find a similar program in reverse; you have to go through ag control on the way OUT, to ensure that no tropical bugs make it back to the states (all of them, not just California).