Of course you can, I do it all the time.
In windows you set the correct flags in DCB in a call to SetCommState, with synaser you call the config method passing false as hardflow (and softflow too, but that's another matter).
Windows api for writing the control lines is EscapeCommFunction and GetCommModemStatus for reading, synaser has the properties RTS and DTR (write only) and CTS,DSR (read only).