As an independent software consultant I create applications for customers that they want with their branding. In particular they don't want the program to show up under the Start Menu in a folder named Syncor Systems Inc. I don't know why not, but you know how irrational those pesky customers can be. When using Click Once deployment it's a simple matter to change the name of the folder.
Right click on your project and select properties. In the resulting dialog click on the Publish tab at the bottom as shown below. Then click the Options… button, make sure the first item Descriptions is selected and change the Publisher name: text box to either their company name or product name or whatever value they want to have show up under the Start menu. And remember the customer is always right even if they won't cater to your ego. At least that's what I keep telling myself.