The connection you get from WebLogic is a kind of wrapper for the direct connection, which adds a few features - for example, connection pooling. Because WebLogic adds stuff to the direct connection, it might be a little bit slower.
It's also possible that your data source in WebLogic is poorly configured so that you get poor performance.
It might also be a bug in your code, or you're not allocating or using the database connections in an optimal way. We'd have to see your code if you'd want help with that.