Protective orders are criminal orders. I think you are referring to a restraining order. If it was denied, it was because there was insufficient evidence to prove physical harm or immediate risk of physical harm.
I don't know what the crime was that he committed but if it is that bad, your next step may be a motion concerning custody and his rights of access to the children.
If you already have custody orders, then you should file a motion to modify parenting time. If you dont have a custody order you will need to start an action to get some relief. the modification order or new action would need to be in proper court form and served by a marshal on the father. The court service center at most courts can help you do this. Remember that if there are no custody orders, and paternity has been established, then he has as much right to have the children as you do until orders enter.
As to the restraining order it appears from your question that you relied upon a newspaper article as your main evidence for the court and that most likely was your problem the article is hearsay. Basically its a statement that cant be questioned by the other side and further wasn't under oath. Im over simplifying but basically it was something the judge couldn't use in making an order. Perhaps hiring counsel in your area to assist you in filing a new restraining order with evidence that can be utilized by a court might be an option.
This information provided is in the nature of general information and in no way creates an attorney client relationship with anyone including the individual who posted the question.
You should have indicated the crime in the first place. I don't know why there was no protective order. One would think that the courts would be interested in protecting children.
In the civil case concerning custody, I would immediately file an ex parte application for custody and I would be specific as to the reasons, including the specific nature of the arrest.