To insert a rewrite rule in to a web.config for deployment purposes you need to modify Web.Release.Config

Example

<system.webServer>
    <rewrite xdt:Transform="Insert">
      <outboundRules>
        <rule name="Add Cross Origin Access">
          <match serverVariable="RESPONSE_Access_Control_Allow_Origin" pattern=".*" />
          <conditions>
            <add input="{REQUEST_URI}" pattern=".*\.(ttf|otf|eot|woff|svg)\?*.*$" />
          </conditions>
          <action type="Rewrite" value="*"/>
        </rule>
      </outboundRules>
    </rewrite>
 </system.webServer>