It's a question that goes deeper than the very simple "counterfeiting is wrong" argument. In this case, there are chips that have the same outward functionality as the FTDI FT232 chips, but which use completely different silicon and don't use copied FTDI hardware. This is legal, up until the point where someone decides to label and sell them as FTDI products, when they then become counterfeit.
However, a fair few of these chips will be buried in devices and may well not carry any FTDI markings at all. It's very common for manufacturers to fit unmarked chips into products, even from legitimate sources, to make the job of copying their product a bit harder.
So, at this point we have the perfectly legal case of a company that has produced a totally different chip, but one that shares the same functionality as the FT232 from FTDI. Where it gets dodgy is with Windows, and only with Windows, as an operating system. FTDI produce the only Windows driver that allows the FT232 to work under Windows. If you run Linux or whatever then there are other drivers that will work with either an FTDI FT232 or with a functionally similar device using different silicon. There is absolutely nothing illegal in using a non-FTDI chip with a non-FTDI driver, or with using an FTDI chip with a non-FTDI driver; either of those cases is completely legal, and doesn't involve counterfeiting, as long as the non-FTDI chips aren't marked with the FTDI logo.
What is illegal is using an FTDI driver (over which they have rights) with a non-FTDI chip. This is what Windows users have had to do, as the only driver that works within Windows is the FTDI one.
Like others here, I suspect, I run a mix of operating systems, from XP on a couple of old PCs, Windows 7 on this PC and Linux Mint on my laptop. If I were to plug a non-FTDI USB to serial converter into the Windows 7 machine, the chances are that the new driver will brick it. This means I can't then plug the same, perfectly legal, USB to serial converter into the Linux machine and use it (well, with a bit of faffing about it seems I might be able to by finding a way to reset the EEPROM inside the chip).
If the non-FTDI chips were counterfeit copies of the FTDI silicon (which they aren't) then I could understand the outrage, as I'm as much against counterfeiting as anyone else. This isn't the primary issue though, the primary issue is that FTDI are trying to stop the use of their proprietary Windows driver with non-FTDI products. This is fine, I wholeheartedly support them in this wish. However, should they have the right to brick a device and so stop it working with drivers written by anyone else?
This is the core of this particular problem, in that FTDI chose to effectively destroy a device that could perfectly legitimately be used in any operating system than doesn't use the FTDI proprietary drivers.
There are a plethora of other issues, surrounding the whole traceability of supply chains. Even the really big and reliable distributors can end up with "fake" products in their legitimate supply chain, without their knowledge. It's even happened to major aircraft manufacturers, where components traceability has been of a very high standard for decades (and orders of magnitude more rigorous than many small electronics manufacturers).
FTDI have acknowledged they have stepped over the line and withdrawn the Windows drivers. My guess is that they realised pretty quickly that a group of, say, Linux users, could sue them for rendering legitimate hardware unusable. What FTDI should have done is use their method for detecting the Supereal chips as being non-FTDI products and stop their driver from working with them. A third party would then have to come up with a Supereal driver, removing the problem (except for those Supereal chips that have been marked up as pretend FT232s).
What will happen now is that, just as with Linux, someone, or a group perhaps, will come up with an alternative Windows driver that works with the Supereal chips. As long as those Supereal chips aren't badged as FT232s there won't be a problem with FTDI.
One slightly ironic thing is that the technology that has been used to make the Supereal chips is slightly better than that used by FTDI, apparently, so with an independent driver and with no FTDI markings on the chips they may well end up being a better chip to use.