I am a website owner, my tax preparer filed my 1099 income on a Schedule C-EZ, why not a regular Schedule C?

You are correct to ask questions about the selection of forms your preparer used. The Schedule C-EZ is a short version of Schedule C and has, in Part II, Line 2, a place for Total Expenses.

Being a web site owner, you surely had enough expenses to justify a Schedule C.

For instance you could automatically have the following expenses or deductions
as a web site owner:

ISP - Internet Provider Service
Online Advertising for your web site
Marketing of your web site
Independent contractors who may have built your web site or upgraded your site.
Monthly fees for email communications
Cost of graphics
Monthly Online services
Mileage to and from the store for office supplies
All office supplies
High speed Internet connection cost
Business cards
Postage
Delivery cost, if any,
Cell phone
Separate Fax Line

Did you work from your home? (Do you rent or own your own home?)
Did you pay office rent? Insurance?
Did you do any advertising offline?
Did you have an eBay store? Monthly cost for e-store
Was there a cost for e-Commerce services?
Did you pay fees to PayPal or another Online Banking Institution?

What about Entertainment?
Did you attend any number of the workshops and seminars for web site owners? And affiliate? (Travel)
Plus, there could be any number of additional expenses as a web site owner.

This seems a little much to put on a Schedule C -EZ - perhaps you might want to keep better records for next year, so that you can take advantage of expenses.

If you need help with your bookkeeping and or tax preparation, let us know, perhaps we can work something out.