Window 2008 server permission issues

You should be able to create a Shortcut and put it in the All Users folder for them to access the site. This shouldn't be a issue with permissions. Make sure that the folder containing the website has permissions for the Authenticated Users to have access or you can just add the Remote Desktop Group to these NTFS permissions.

Your rdp users would not need any special permission except  access to internet explorer.

The authorisation to access the site is controlled via IIS (and depending on how IIS is setup, at the file system).

It is not a website. It is like a webserver/application . I don't know if the term i am using is correct. But the application is running on that particular port. The developers believe it is the permission issues since domain admins can open the application on that port just fine. But terminal server users are unable to run application through that port

The developer told me to read in this article
http://technet.microsoft.com/en-us/library/cc786389.aspx
but it only apply to windows 2003 and we are running on 2008

If it is a web application then it is a website as well and the path to the web application should is part of IIS. If you look on the permissions of the web application that contains the data to be displayed in Internet Explorer should have authenticated users in the permissions of the content folder. Look in IIS look under your Websites and see if you see the application listed right click on the folder and select browse to so you can see where the folder content is located to check folder permissions.

hmm the article you posted talks about installing certificates in client profiles. Does your application have a valid ssl certificate or is it self signed ?

There may be some security restriction for your rdp users where sites they visit require valid ssl certificates.

You could verify this (assuming you have a self signed certificate) by installing the SSL certificate from the web server into the trusted root certificates store of a normal rdp user (not admin).

There may also be something in the security policy (firewalls/routers) that prevents users connecting on not standard SSL ports (not 443).  We recently had an issue where a company in China could not access our application using non standard SSL ports because of the 'great firewall of china'.  

Hope this helps.

Also it might help us to know a little bit more about your application ?
What languages/platform  ?
Is it a clickonce deployment ?

Yes. It is a self signed certificate. The users are accessing it via terminal server web or remote desktop. I believe the application is written in .net and it is a clickonce deployment set up. as far as port being opened on the firewall i only have 3389 80 and 443 open. It is a cisco box. But what i dont understand it that if they come in though remote desktop would it look like they are sitting on the server? and not from outside ?? so with 2008 does it have a folder like wwwroot or intpub?? i am not too familiar with the 2008 lay out