My question will be, why would a company develop a product that uses the manufacturer's default VID and PID, knowing that any program that can talk to a COM port could cause damage or be dangerous?
Nah, those products are done by cheap and hobby level products and won't invest in making sure their device is bullet proof.
Regardless of FTDI or whatever other chip is used.
If the product uses the FTDI chip, it is the simplest way to use the manufacturers VID and PID, because otherwise you would have to provide an INF file (which needs to be signed for newer Windows versions), which would simply reference the ftdibus.sys driver anyway. As I've tested, the standard Microsoft usbser.sys doesn't work with the FTDI chips.
I think there is nothing wrong with protecting the IP. I really like the functionality of the FTDI chips, especially the modern versions, like the FT2232H, which you can use as a JTAG programmer as well (supported out of the box by the Lattice FPGA programmer). It is some work to produce a good working chip with driver support for all operating systems that usually just works. Cheaper alternatives are not as good, like the MCP2221, which has a
gap of 30 us between bytes, so it is useless for modern higher baud rates like 1 Mbaud and even at 115,200 baud the effective baud rate will be solwer than possible.
Of course, it is another question how to protect the IP. Providing test tools, even displaying a warning for counterfeits is ok, but the product should still work, even if it uses a counterfeit. Or maybe show a warning which says that it will stop working after a month. Then the users have time to replace it, or get the money back from the eBay sellers.