It depends on how much weight you would apply to the following questions:
As a user, should I be able to deactivate the automatic startup easily, even temporarily?
As a user, should I get the feeling that the developer trusts me to know what I'm doing?
Clarification:
If I have a shortcut in the AutoStart folder, I know that I can quickly disable this part by myself and the developer trusts me to do this.
If I don't have this visual clue, I have to actively look for it using more-or-less arcane tools (speaking from experience here).
If the automatic startup is essential for the correct function of the program, by all means, put it somewhere I can't get to it. But if it's a nice-to-have thing, like a "quickstarter", then please don't.