The State Department FAQ page covering this explains the limited uses for the Passport card as follows:
The passport card was designed for the specific needs of northern and southern U.S. border communities with residents that cross the border frequently by land. The passport book is the only document approved for international travel by air.
Final rule covering this can be found at 72 FR 74169, which includes further explanation of the rulemaking process used, and says:
The passport card was specifically designed to respond to the concerns expressed by border communities in regard to the requirements of WHTI. The passport card is designed specifically to address the unique circumstances of land border crossings and is not intended to be a globally interoperable travel document. Therefore, passport cards will not be designed to meet the International Civil Aviation Organization (ICAO) standards and recommendations for globally interoperable passports.
Because the passport card will be specifically designed to facilitate land and sea border crossings, it is not compatible with the global air environment, which is already set up for passport books. In addition, extending the use of the passport card to the air environment could create confusion with the traveling public should they attempt to use the passport card for travel to a country other than Mexico, Canada or the Caribbean.
The paragraph citing International Civil Aviation Organization standards probably best explains the restriction, but rather than view this as an restriction, it might help to view this as targeted relaxation of rules for residents of the border communities, who prior to WHTI could drive across the border at no cost, with appropriate locally-issued identification. A number of border states, starting with the State of Washington, were able to offer an alternative, the 'enhanced drivers licenses' which homeland security eventually decided to accept. In Washington state, travel to/from Canada via boat is fairly uncommon, which probably explains why the passport cards are also acceptable for "sea" use.