You should check your product configuration file (*.product). The path to icons should be relative to product project. So for example with project:
com.myapplication.product/
myProduct.product
icons/
application.ico
your myProduct.product file should look like this:
...
<launcher name="executable">
<linux icon="icons/application.xpm"/>
<macosx icon="icons/application_32.icns"/>
<solaris/>
<win useIco="true">
<ico path="icons/application.ico"/>
<bmp/>
</win>
</launcher>
...
Check this sample of tycho product configuration: https://github.com/jsievers/tycho-demo/tree/master/tychodemo.product