It never ceases to amaze me how software developers are so keen that we install and use their software exclusively, and spend tons of money getting it right, then they fail to provide us with a suitable uninstall procedure.
I don't think there is an easy way to remove this file. If you are talking about the startup file in MSCONFIG, then unchecking it is usually enough. You can also hunt down any remnants of the software and remove those folders and files.
To remove that entry from MSCONFIG may need delving into the registry, but that is something I wouldn't normally suggest. Such entries may appear in the Registry under the "Run" keys, as described here; http://support.microsoft.com/kb/314866, but if you intend to remove them manually I would suggest you find out more about the registry, how to back it up, and hw to restore it, if anything goes wrong.
That Microsoft article is based on Windows XP. I assume that is what you are using.
You could use a utility like CCleaner, from http://www.ccleaner.com, which has a "Check registry" option, and that will often be able to remove any orphan "Run" entries, and also offers a registry backup option.
I hope that helps.