The main difference between the loan that Antonio has given Bassanio and the loans that Shylock gives out is a question of interest. In Act 1, Scene 3, Shylock clearly indicates that Antonio frequently gives out interest free loans.
He lends out money gratis and brings down
The rate of usance here with us in Venice.
Shylock is a money lender that charges interest. When Antonio gives out a loan and doesn't charge interest, he is undercutting Shylock's business and possible profit margins. That is one reason why Shylock does not like Antonio at all. Shylock's loan to Bassanio is different from Antonio's loan, because he charges interest. What is unique about this one time loan though is that Shylock forgoes the payment of interest. He does that in exchange for the right to take a "pound of flesh" from Antonio if the loan cannot be repaid.
This kindness will I show.
Go with me to a notary, seal me there
Your single bond; and, in a merry sport,
If you repay me not on such a day,
In such a place, such sum or sums as are
Express'd in the condition, let the forfeit
Be nominated for an equal pound
Of your fair flesh, to be cut off and taken
In what part of your body pleaseth me.