I guess this isn't "doing it programatically with C#", but you could jQuerify the page, then run some custom javascript afterwards, to manipulate the value of the control. If you are using WebBrowser, you could call the below method to insert the scripts.
string script = "script text";
WebBrowser.Navigate(script);
jQuerify code
var s=document.createElement('script');
s.setAttribute('src','http://jquery.com/src/jquery-latest.js');
document.getElementsByTagName('body')[0].appendChild(s);
Custom code
$(document).ready(function(){$('input[type="text"][name="user"]').val('FooBar')});