The verse your article talks about is Nehemiah 5:10 which says:
I likewise, and my brethren, and my servants, might exact of them money and corn: I pray you, let us leave off this usury.
Some translations also say "interest" in place of "usury." This is an important distinction... A prohibition against usury is only a prohibition against "exorbitant interest" in modern English. This would be one reason the verse is not interpreted as forbidding the charging of interest.
However, I think the more important thing is to take the verse in it's larger context. The verse comes in the middle of a story about a famine, where people were literally in danger of starvation. They were mortgaging their "fields, vineyards, and homes" to be able to afford to buy grain. These people were hanging on by a thread, and in desperate need of help.
The response of many of the Jews was to lend money, at an interest rate (of 1% according to verse 11, although 1% per what time period?).
Nehemiah's anger appears not to be at the specific fact that they were charging interest, but at the fact that these Jews were not being charitable.
Not only did Nehemiah demand that they stop charging interest, but also that he give back their collateral--and with no mention of being repaid. The people's response is (verse 12) "And we will not demand anything more from them." This also seems to indicate that they did not demand repayment of their loans.
If we are to apply the principles of this story to every situation, then not only should Christians not charge interest, but they also should not even ask to be repaid when they make a loan.
I hope it is apparent that this is not the intention of the story, but rather the intention is not to take advantage of people in need.