I should say they don't have
real reasons, but they have plenty of weak ones. They see their toolchains as part of their competitive advantage, which is weird because FPGA toolchains are some of the most annoying software applications around. The market as a whole could only benefit from additional third party involvement.
Especially at the high end, the manufacturers commonly introduce new hardware constructs -- high-speed transceivers, clock generators, memory controllers, that kind of thing -- and they don't really want to document and disclose the inner workings of these components at a level that would allow third parties to write tools for them. It could potentially take a non-trivial amount of documentation and customer support work. Meanwhile they want to preserve their trade secrets, and they also don't want to attract infringement suits from either patent trolls or legitimate competitors. Disclosure of bitfile formats would open those particular kimonos a bit too wide for comfort. This is largely why Linux users can only get GPU support via binary blobs.
At the low end, some good reverse-engineering progress has been made by people like Clifford Wolf on the Lattice parts. This work is certainly important, but as long as there's reasonably rapid technological progress on the hardware side, reverse engineering is never going to be enough to sustain a healthy third-party tools industry.
It's a real shame. Imagine how far we'd (not) have come if Intel and Motorola had walled off their instruction sets...