It is a well-known fact that Shankara rejected both Vaishnava and Shaivite Agamas. However, I got to know from a friend that the philosophy of Bhairava Agamas were similar to Shankara's Advaita Vedanta philosophy. Did Shankara reject all Shaivite Agamas including the Bhairava ones?
Yes, Adi Shankaracharya was opposed to the Bhairava Tantras. Adi Shankaracharya sent his shishyas to defeat the followers of the Bhairava Tantras, as described in this excerpt from the Madhaviya Shankara Digvijaya:
Now Acharya Shankara, along with the king Sudhanva and a large number of disciples, started on a Dig-vijaya - a missionary tour for the propagation of the Advaita doctrine by controverting all philosophies opposed to it.... Next, blessing the people of Andhra country and worshiping Lord Venkatanatha, he reached the land of Vidarbha. He was given a cordial reception by the king of that place. There, Padmapada and other disciples engaged themselves in controverting the perverse doctrines of the Bhairavas.