Does anyone live in the C3 where you are trying to run the sites? Are you not scanning down the chains and finding whats on the other side of the WH's that also connect to the C3?

WH space is far more active than null space. You'd be much better off joining an Null Alliance and run anoms in their region.

To be honest I wouldn't let that stop you, more often than not you'll find every connection's already been popped.

Low class systems do tend to have quite a bit of traffic, really depends on what your static(s) are. But in general, yeah you're going to have people passing through quite a bit. You've ran sites twice and had someone hunt you both times, with only that to go on it's kinda hard to tell if you're doing something wrong or just got unlucky. Try twenty times and see if you keep getting jumped, that might give you more of an idea if you're doing something wrong. For instance, for all you know you may have been running sites in a hole that's right next door to major pvp corporations both times and you wouldn't have known as you didn't scout the connections.

Situational awareness is key, scanning down as much of your chain as you can, seeing which holes have active pilots sitting around at their POS, if those corporations present a threat and (best thing ever for safety) keeping alts cloaked on the connections into the system while you're farming it, listening for wormhole activations so you can get out of site before the bad things come.

So what you're doing is running sites in a random system, without scanning it, with no idea what it's connected to and you're asking why you're getting ganked?

Yeah, see, this is EXACTLY why I tell people to join an existing wh Corp if they have no idea what they're doing.