1) I'd add a /n after init. i.e. write( USB, "init\n", 5);
2) Double check the serial port configuration. Odds are something is incorrect in there. Just because you don't use ^Q/^S or hardware flow control doesn't mean the other side isn't expecting it.
3) Most likely: Add a "usleep(100000); after the write(). The file-descriptor is set not to block or wait, right? How long does it take to get a response back before you can call read? (It has to be received and buffered by the kernel, through system hardware interrupts, before you can read() it.) Have you considered using select() to wait for something to read()? Perhaps with a timeout?
Edited to Add:
Do you need the DTR/RTS lines? Hardware flow control that tells the other side to send the computer data? e.g.
int tmp, serialLines;
cout << "Dropping Reading DTR and RTS\n";
ioctl ( readFd, TIOCMGET, & serialLines );
serialLines &= ~TIOCM_DTR;
serialLines &= ~TIOCM_RTS;
ioctl ( readFd, TIOCMSET, & serialLines );
usleep(100000);
ioctl ( readFd, TIOCMGET, & tmp );
cout << "Reading DTR status: " << (tmp & TIOCM_DTR) << endl;
sleep (2);
cout << "Setting Reading DTR and RTS\n";
serialLines |= TIOCM_DTR;
serialLines |= TIOCM_RTS;
ioctl ( readFd, TIOCMSET, & serialLines );
ioctl ( readFd, TIOCMGET, & tmp );
cout << "Reading DTR status: " << (tmp & TIOCM_DTR) << endl;