This is a weird one. The hold short line is supposed to be far enough from the runway to prevent a collision if used correctly. Since neither the student nor the controller verbally confirmed that adequate clearance from the RJ would be maintained, if anything had happened it wouldn't have been good for anybody. It sounds like the controller was ok with the spacing from their vantage point.
This could have easily become a scary situation in my opinion. I think the tower should have confirmed adequate spacing with the student pilot or given a caution statement or something of the like. Reminds me of the L.A. accident, where the controller cleared an aircraft to position and hold on a runway at night and forgot about them, leading to the fatal collision from an another airplane landing on them.
Goldmember, did you tell them that you were a student pilot, over the radio? I don't like it when controllers assume that we know what they're thinking. It makes me nervous. Of course, 99.9 percent of the time, controllers are very professional, though

. But, if that controller had at least clarified to Goldmember that they could see that they were across the hold-short line and that it was ok, then Goldmember wouldn't have been so confused. If the controller couldn't tell from their vantage point, then shame on the controller for not confirming!!
That's not to say that anything necessarily bad happened there, but I'm a big fan of not getting lazy on the ground. We have a lot of incursions happen here in Milwaukee, because of people not paying real close attention to what's going on. A simple clarification from either end could prevent an accident. Preventing incursions should start with the very simple situations like this, not just major mistakes. Assuming is bad.