This is one of those I am not a lawyer questions as such ultimately if you feel strongly enough you should consult with one.
However the image on that site is licensed as http://creativecommons.org/licenses/by/3.0/ which can indeed be used for commercial use. If the author wishes to change the license he is responsible for identifying and updating those locations. As licensed you are free to use it and their isn't anything he can really do about it. If he does have any legal recourse it would be more likely to be with softicons assuming they have ignored his request for his work to be removed. The license does clearly state that the author has the right to release the work under a different license, however work already in use with this license may continue to do so.
Subject to the above terms and conditions, the license granted here is perpetual (for the duration of the applicable copyright in the Work). Notwithstanding the above, Licensor reserves the right to release the Work under different license terms or to stop distributing the Work at any time; provided, however that any such election will not serve to withdraw this License (or any other license that has been, or is required to be, granted under the terms of this License), and this License will continue in full force and effect unless terminated as stated above.
That said, the author has made it clear to you that even though he licensed his work one way he desires something else. It's up to you to decide if it's worth discussing with him/arguing with him, using it anyway or just seek an equally nice icon. It may well be that you decide its not worth the hassle of dealing with an irate author and any associated publicity.
Standard IAMNL disclaimer begins