Other than most of the EXP boards with internal FET, the standalone FET430UIF does not support an application UART. The COM-port you see is only used for communication between PC and the FET.
To see the serial output of your target board, you'll need to attach a separate SER/USB converter or a RS232 level shifter like the MAX3232 (to connect to a real COM-port).
CCS provides a 'console' which intercepts data sent to printf by 'fetching' it from the running code through JTAG. However, this feature is not available outside CCS, for matlab, you'll need a real serial connection.