I would be skeptical of the article you read. The TOR Browser Bundle (TBB) is safe in most instances. The admonishment to not use Windows if possible is a good one, but unless you are doing some really bad stuff, it is probably "safe enough" (Linux is always preferable though).
In years past, the TOR browser bundle lacked certain security patches in Firefox that could have been exploited to uncover the identities of people using it. However, it was likely only three-letter-agencies (e.g. the NSA) who were doing that on any meaningful scale and current versions of the software purposefully try to keep up with security patches to minimize the amount of time a certain browser version might be vulnerable. That said, I've never read anything to make me believe the Freedom Hosting takedown was due to the TBB. That was almost certainly other things.
Regarding a "standalone" version of TOR, they were likely referring to the Windows Expert Bundle. (As an update, since the article says they don't like Windows, they apparently mean "Use some version of TOR, just not the prepackaged TBB which includes Firefox.")
It is possible to setup TOR manually to work with a browser of your choice but it is a decidedly technical pursuit for many average users. And unless you genuinely know what you are doing, it is likely easier to misconfigure the "standalone" version which may leak details about you and your session. What the TOR Browser Bundle does is package a version of TOR with a preconfigured version of Firefox, both of which install easily for most users and are generally secure.
But...
The only genuine caveat concerning the TOR Browser Bundle is that current versions have some features left on by default which should really be turned off for anonymity. The reason these features are left on is because certain "regular" websites will "break" (not work correctly) without them.
However, it is entirely possible to "switch off" these features (which generally aren't needed for sites on the TOR network, which exclude the need for these features purposefully to help anonymity). But unless you are looking for them, it is possible to leave them on and expose yourself.
Updated July 2019 For Tor Browser Bundle v8.5.4 (Firefox 60.8.0 ESR)
To start, right-click the uppermost portion of the browser window and enable the Menu Bar. Then under Tools -> Options -> Privacy & Security (about:preferences#privacy), make certain the following items are set correctly:
Under History, ensure Use custom settings for history is selected. Always use private browsing mode should also be enabled.
Under Cookies and Site Data, mark the Block cookies and site data option.
As a matter of course, under the Address Bar section, I would uncheck all three options (Browsing history, Bookmarks and Open tabs). You likely don't want to keep a history of what you type in the address bar if you really care about privacy.
Set Tracking Protection to Always. (Recommended)
Under Permissions, check Prevent accessibility services from accessing your browser. (Recommended) [You will be prompted to restart the Tor browser if you check this option.]
Under Security, mark the Safer or Safest option (the higher the better). You can click the Shield Icon on the toolbar (in the upper right corner of the browser) then click Advanced Security Settings... to quickly access these options in the future.
The NoScript add-on bundled with TBB previously had a separate toolbar icon, but that seems to have been removed in current versions of the TBB. Instead, choosing the Safer or Safest options (above) will disallow scripts, etc. (either on non-HTTPS sites [Safer] or entirely [Safest]). NoScript also has a number of options you may wish to investigate under Tools → Add-ons → NoScript Options.
After adjusting these settings, I would suggest restarting the Tor browser and checking out JonDoNym's IP Check and the EFF's Panopticlick. Also, remember to recheck these settings periodically, especially after upgrading the TBB.
If you are really privacy minded, you should consider The Amnesiac Incognito Live System (TAILS), which is a Linux Live CD which offers excellent security for TOR browsing. I would not recommend it in a virtual machine, however. (The best use of the Live CD is on a PC without a hard disc at all, at least in my opinion.)
Reference Article Originally Cited:
http://www.hongkiat.com/blog/do-donts-tor-network/
