The stuff the article is talking about is real, but it's not even that new, and it's very limited in scope.
Data leakage via the cache: yes, it's true that another app on the same machine can carry out a timing attack to painstakingly gather data, bit-by-bit, from the cache. It takes a huge number of CPU cycles but on a modern CPU that's still very little time. But it has to be running on your machine to do this. So net result: if you have malware on your PC, it can steal your data even if you encrypt it.
This said, the attack is cryptographically challenging, and nobody encrypts stuff, so a malware author actually carrying this attack is like a burglar breaking into your house by digging a tunnel into your basement -- sure, it can be done, but it's easier to just break a window. Saying that cache timing attacks make "all your security worthless" is like saying that bulletproof vests are worthless because they won't protect you from a nuclear missile.
There's a simple rule: if someone else can run arbitrary code on your computer, it's not your computer. Don't run shit you shouldn't, and if you're going to run something shady, do it in a VM. (Yes, VM jailbreak attacks exist, but they're also challenging and malware doesn't bother because malware's primary target -- i.e. idiots who install Anna Kournikova screensavers they got in spam email -- doesn't use VMs.)
Crypto systems like TrueCrypt, BitLocker, etc. are valuable for protecting your data from physical theft. They keep people out of your data even if they steal your laptop or hard drive. They will not, however, protect you from malware installed on your PC.
