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Connected and automated vehicles (CAVs) provide various valuable and advanced services to manufacturers, owners, mobility service providers, and transportation authorities. As a result, a large number of CAV applications have been proposed to improve the safety, mobility, and sustainability of the transportation system. With the increasing connectivity and automation, cybersecurity of the connected and automated transportation system (CATS) has raised attention to the transportation community in recent years. Vulnerabilities in CAVs can lead to breakdowns in the transportation system and compromise safety (e.g., causing crashes), performance (e.g., increasing congestion and reducing capacity), and fairness (e.g., vehicles fooling traffic signals). This paper presents our perspective on CATS cybersecurity via surveying recent pertinent studies focusing on the transportation system level, ranging from individual and multiple vehicles to the traffic network (including infrastructure). It also highlights threat analysis and risk assessment (TARA) tools and evaluation platforms, particularly for analyzing the CATS cybersecurity problem. Finally, this paper will provide valuable insights into developing secure CAV applications and investigating remaining open cybersecurity challenges that must be addressed.