The last thing I want to do here is make you feel like we are piling on, but someone's gotta say it:
While your frustration is completely understandable, and we all have the greatest sympathy, the first thought that occurs to most of us is that you want to fix a rattling engine by driving your car (and yourself) off a cliff.
If you do have a virus nested in your system through WINE, then it got there precisely because Windows programs are built to demand system privileges to function and Windows idiotically gives it to them. You are now asking for instructions to totally hose your Ubuntu security and bring it down to a Windows level so that you can deal with a virus that exists only because Windows starts out with a hosed security model. That reasoning just blows my mind.
You are looking at Linux restrictions as impediments. In fact, they are the very safeguards that make it tough for nasties like the virus you are currently dealing with to infect Linux systems. If you find it difficult to chown and chmod, to say nothing of gaining root privileges, then a piece of dumb malicious code certainly won't be able to do it. And this is the very safeguard that you now want to dismantle.
The members of this forum are happy to help you deal with whatever problems you are having. Deleting whatever is in an infected directory is not really that difficult. But, speaking only for myself, I've resolved not to give instructions that dismantle the Linux security model. The last thing we need as a Linux community is security that's as lousy as Windows'.
Re: virus in directory. You can delete the whole directory with:
Re: More powerfully, hit <Alt>+<F2> to bring up the run application dialogue box. Doing:will invoke nautilus in root mode and let you delete every directory in creation, from root on downwards if you so wish. Want to delete hidden directories too? Just <Ctrl>+<h> to unhide them. Now you can go to town on those too.
sudo rm -rf /path_to_directory/.Trash-999
No one is telling you that you can't have access to your own system. The two simple commands above give you all the access you could wish for. The irony is that Linux is actually the system that lets you do anything you want. If anyone is denying you access to your own system, it's the proprietary OSes who won't let you change a shred of their code (but that's another discussion for another day).
It is much more accurate to say that Ubuntu puts safeguards in place to prevent people from doing dangerous and stupid things to their system and to their data. chown and chmod are part of a system that prevents baddies from looking at your private files. sudo is designed to make you pause before inadvertently deleting your whole installation (as I did when I first started in Linux and harboured exactly the same misconceptions that you now have). If you work with these features rather than fight against them, you will find that they repay your time and effort with advantages you never dreamed of. And the members of this forum are more than willing to help you get there.