One problem these counterfeit chips pose is that all the sudden companies like FTDI end up with a lot of support costs for people who bought shoddy products with the fake chips, which often don't work nearly as well as the real thing. This is a way for FTDI to crack down on the counterfeit chips. While it sucks for the consumers that end up with the fake chips, it will also help put a stop to the counterfeit chips since any product that uses them will not work.
At my company we make a number of development boards using the quad FTDI chips for the serial interface. We use them because in addition to RS232 they also can talk I2C and JTAG, among other things. I can reliably run the FTDI chips at 10Mbps. I've used other USB to serial devices in the past but I've had lots of problems with them. Some cables I bought, for example, will just suddenly stop working and I have to periodically reset the baud rates.
Why should FTDI have to bear the burden and support costs of counterfeit chips? If somebody else slaps the FTDI manufacturer ID and product ID onto their USB device then they deserve whatever happens. Why should FTDI have to spend resources supporting fake chips? By doing what they are doing, it will drive the fake chips out of the system and prevent future ones.
I work for a chip manufacturer and while there's a very low risk that someone will make fake chips like ours (very complex network processors), we have had to add features to our chips so that our end customers can prevent counterfeit equipment which just copies their software. We have some large customers who have been battling Chinese made counterfeit equipment.