So I was reading a email newsletter that says querying production companies on your own can hurt your script more than help.
The only reason I would consider it bad is because your rep wants to control who has seen your script. No one wants to go out with a script that all the studios have passed on, or seen. That's why they ask you who has read it when they court you.
So, from that perspective it can be detrimental; however, you do what you have to do to sell your story.
If you plan on getting repped, then I would only query managers/agents, not prodco's initially. If that doesn't work, mix it up, but never give up.
Of course, I know repped people who query without their reps, so to each their own.