The article is missing a critical fact. What operating system were the banks that were victimized running? My guess is that the operating system that was infected with malware was some version of Microsoft Windows. In this case the issue is no different than the many Bitcoin users who have had their Bitcoins stolen because the used the same operating system.
The real issue here is not Bitcoin vs fiat but rather the choice of Microsoft Windows over GNU/Linux that has made the banks victims in this case for the very same reason that many Bitcoin users have also been victimized
Some of the largest hacks in Bitcoin history have all involved services running on Linux. Security is a mindset not an OS. MtGox, BitStamp, Coinflor, MyBitcoin, Bitcoinica, Slush, the Bitcoin faucet (the original), etc. What did they all have in common? They all ran on Linux and they were all robbed blind.
Sure but they have more often than not involved poor password security, overall poor server security and not OS specific malware. Yes of course security is a mind set but it begins with picking the right OS. The types of attacks that targeted the banks and many hacking attacks involve planting malware on Windows desktop computers that is then used the steal credentials. These stolen credentials may actually be used to attack, a GNU/Linux server, but even in this case the fault lies with Microsoft Windows. This is possible not only due to both the design of Windows but also because of how Windows is marketed particularly to consumers. The latter is what makes possible the massive fertile ground of vulnerable Windows computers that allows Windows malware to breed. How many Windows computers are sold to consumers that treat security as an up sell? The economic incentives in propriety software distribution actually encourage the end user to seek the Internet for gratis alternatives. They also make it easy to install software on Windows, while forcing users and administrators to have to seek software from all over the Internet. I have seen very experienced Windows administrators get fooled into installing malware. The alternative to this malware cesspool that is provided by Apple and Microsoft is an Orwellian lockdown where only applications approved by big brother can run. This leads to yet another problem since it encourages users to break the security of the OS wide open to get the freedom they deserve.
Now compare this with GNU/Linux where users and administrators are provided with a trusted software repository with 99% of the software most users will need is available gratis. Getting software to run from outside the trusted repository is possible but nerdy. It invloves in many cases compiling the software from the source code. Even if an executable is available and it matches the right distribution it still involves manually changing a set of permissions on the executable file. So Joe novice tries to install a malware executable on GNU/Linux. The most likely result is that he gets an obscure error and contacts technical support who promptly sets him right.
Security is not just about the user or the OS, it is also about the entire ecosystem.
Edit: GNU/Linux is about
source compatibility since it is designed for FLOSS. Microsoft Windows is about
binary compatibility since it is designed for propriety software. Malware does not spread very well if it has to be compiled by hand.