The prohibition against usury in the Bible was generally against charging interest to the poor and to fellow Jews. Just a few examples:

Leviticus 25:35-36 -- "If your brother becomes poor and cannot maintain himself with you, you shall support him as though he were a stranger and a sojourner, and he shall live with you. Take no interest from him or profit, but fear your God, that your brother may live beside you."

Deuteronomy 25:20 -- "You may charge a foreigner interest, but you may not charge your brother interest, that the Lord your God may bless you in all that you undertake in the land that you are entering to take possession of it."

Moreover, Jesus speaks positively of those who invested their money wisely in the parable of talents, and to the one who didn't invest, explicitly said, "You ought to have invested my money with the bankers, and at my coming I should have received what was my own with interest." Now, the parable is indeed a metaphor for things beyond money, but it's unlikely he would have spoken positively of investing with interest if it was absolutely forbidden.

Both Catholic and Protestant traditions also understand usury to mean taking advantage of those in need (which I think is consistent with the Old Testament prohibitions), rather than charging interest on a loan which is intended as a mutually beneficial commercial endeavor.