Msconfig is not the preferred way to troubleshoot general startup item issues. It's mostly for bigger problems, but yes, you can use it. And uninstalling is an option IF the program has an entry in ADD/REMOVE programs.
Using autoruns effectively uninstalls an application in the sense the it no longer runs. It's still present on the system, but not loading.
I use it (for one example) to demonstrate to clients how much their anti-virus is slowing down their machines. I totally uncheck (disable) all Norton or Mcafee functions and then reboot their PC. They are amazed how much faster it boots.
Then, I re-enable Norton/Mcafee/Whatever and show them what they were living with. Then I sell them something better - usually Windows Live One Care or AVG 8.0 Free if they're cheap.
Autoruns is also great if a program's uninstall feature is broken. You can snuff out all the little bits and pieces that start up, then you can delete folders manually and then clean the registry. Not the preferred way, but it works to remove things.