Obviously you misunderstand something. You do not have to insert
index.php? by yourself.
If you put the link
<a href="[[~2]]">Go to our product line one</a>
in your template, running the preview and hovering the mouse over
Go to our product line one will show you in the statusline that MODx automatically creates this link:
http://www.example.com/index.php?id=3
- the work is done by MODx! That is, essentially, the reason why you use a CMS...