Some say that studying/reviewing torah online can be harmful as there are many unreliable sites, but i see that torah.org, chabad, etc are reliable ones. Can anyone recommend how to best learn Torah online, safely?
I have to refute your premise. View the numerous yeshivot that post shiurim online. As a matter of fact, several programs such as web yeshiva not only place shiurim online but offer semicha (Rabbinical ordination) by studying online.
I've listed just a small sample of what's out there. You mention Chabad.org. I assume, then, that you have visited parts of their site and noticed how many shiurim such as Ramba"m, Tanya, parsha and others are on their site. A number of rabbis have put this together, no?
Apparently, there are, then, many rabbis that are allowing studying Torah online! Among them - Chabad rabbis!
In my neighborhood, I deal with 3 different rabbis on a frequent basis. Additionally, two others that I speak to frequently run yeshivot. All of them give numerous shiurim, and I know that they get much of their own materials from the web. The two that are Roshei yeshiva encourage their own students to use the web to find Divrei Torah and they as well as the rebbes who teach there tell their students to do the same. So, it seems to me that you have in my neighborhood alone, close to 100 rabbis using and encouraging others to study Torah on the web. If you expand this statistic to what occurs in many other neighborhoods throughout the U.S., I think that you will have a few thousand.
The Torah (I assume that's what you mean by "our book") of course has no reference to the web for one main reason. The web didn't exist at the time the Torah was given.