First, a government agency is not going to have a .net address. They always use .gov.
"The site does not make it clear it is a paid service, their disclaimer does not state it it a paid service, they make it look like the IRS."
They state right on the home page : "This site is not affiliated with the US Department of the Treasury or the IRS" and their terms of service page pretty clearly states that they charge fees. I would think that the requirement to give them your credit card info would remove all question that it is a paid service. In other words, the site does make it clear, you just didn't bother to look.
I'm not saying that it's OK for a company to charge for what is essentially a free service from the IRS. They obviously make their money from people who don't bother to do any research before handing over payment. The Internet is full of sites like that.