For changing the zoom level you can use the following set of statements:-
DesiredCapabilities caps = DesiredCapabilities.internetExplorer();
caps.setCapability("ignoreZoomSetting", true);
driver = new InternetExplorerDriver(caps);
I am not sure about the protected mode setting but here is a solution I found on GitHub:-
https://github.com/seleniumhq/selenium-google-code-issue-archive/issues/4249
Hope this works.