You can play mkv files in PS3 but not from usb input you need to transfer mkv file from computer to PS3 Hard drive through LAN servers for eg. PS3 Media Server.
How to do that,
Install http://ps3mediaserver.googlecode.com/files/pms-setup-windows-1.20.412.exe in your Windows PC (this is beta version)
Start Server in your PC it will find PS3
Go to your PS3 Video select server
Navigate to file then press Triangle then select copy (this will copy mkv to ps3 hard disk)
Enjoy your mkv video.
How to do that,
Install http://ps3mediaserver.googlecode.com/files/pms-setup-windows-1.20.412.exe in your Windows PC (this is beta version)
Start Server in your PC it will find PS3
Go to your PS3 Video select server
Navigate to file then press Triangle then select copy (this will copy mkv to ps3 hard disk)
Enjoy your mkv video.