You should be able to set a [defaultFilter][1], or once the filter is created you can use [mergeWithDefaultFilter][2]. 

	
    var protocol = new OpenLayers.Protocol.WFS({
        version: "1.1.0",
        url: MapBase.Configuration.GeoServer.WFS_Service.EndPointURL,
        featurePrefix: MapBase.Configuration.GeoServer.WFS_Service.featurePrefix,
        featureType: MapBase.Configuration.GeoServer.WFS_Service.featureType,
        featureNS: MapBase.Configuration.GeoServer.WFS_Service.featureNS,
        geometryName: MapBase.Configuration.GeoServer.WFS_Service.geometryName,
        defaultFilter: myFilter
    });

    protocol.mergeWithDefaultFilter(myNewFilter);


  [1]: http://dev.openlayers.org/docs/files/OpenLayers/Protocol-js.html#OpenLayers.Protocol.defaultFilter
  [2]: http://dev.openlayers.org/docs/files/OpenLayers/Protocol-js.html#OpenLayers.Protocol.mergeWithDefaultFilter