Agreed but...
My real worry was that malware could hide in the Fonts folder and it would be "invisible" to most users (i.e. users who don't know about the Command Prompt). 
Malware is already invisible to most users even if they go looking for it. The files for malware look no different then any other file on your computer. This is why we have malware scanners. Malware could hide its file in a log directory and you would not even know, would you? It could still have the same ".log" extension and everything.
Agreed, but if I saw a log file running in Task Manager or Process Explorer, I would be suspicious (not much help for the average user though).
I have encountered malware that couldn't be removed by my anti-malware programs (back in the bad old Windows 98 days) and I had to hunt down the files and registry entries myself (painful).
My real worry was that malware could hide in the Fonts folder and it would be "invisible" to most users (i.e. users who don't know about the Command Prompt).
they could be anywhere. their favorite place so far usually temp folder and system 32,that is based on my exp
Agreed, that's where they usually hide.
In the past, I have seen mysterious processes running (in Task Manager or Process Explorer) and I have navigated to the location using Windows Explorer and then killed the offending file.
I have had malware install itself in the saved game directory of a game (conventional not online).
Obviously those were amateur malware attempts.
My opinion is that a file manager should show you the files that are on your system.
It shouldn't just decide at random that "you don't need to know".
That's one of the things that Linux users complain about Windows doing (Windows knows best, hands-off stupid user).
How many other folders exhibit the same behaviour as the Fonts folder?
I can view files in the System folders (assuming that I choose the appropriate folder options).
If any files should be "invisible", surely it should be the System files.
