>And in the name of protecting the user from malware they have no tools to deal with it
There are tools as the ecosystem is open and the community is extraordinarily talented, but it largely depends upon the device, whether the kernel source, driver blobs are available and boot loader can be unlocked; these were generally true for most devices from high profile manufacturers, but now things are changing as those manufacturers have ventured into $1000 smartphones and don't care for their enthusiast population.
Then again, new breed of pure Linux smartphones are available now. IMO, this should be the long term focus for any enthusiast wanting a free, open, secure mobile computing experience.