Unfortunately this is a known limitation of the Site.com platform. The CSS parser that is being used does not support some of the newer CSS3 features, such a media queries.
There are a couple of workarounds available if you can't wait for salesforce to fix the issue. These workarounds won't show the styles in the studio (like when you use the CSS editor), but when you preview the page they should be visible.
Import an external style sheet in the Head Markup

By selecting the page and then clicking Edit Head Markup under Scipts (see image above) you could add a reference to an external style sheet that contains any CSS you want using a link like the following:
<link rel="stylesheet" type="text/css" href="mystyle.css">
Include a style directly in the Head Markup
Using the same steps as above, you could also add your CSS3 styles directly on to the page:
<STYLE type="text/css">
@media screen and (device-width: 800px) { color: red; }
</STYLE>
Use a Custom Code block
Markup in a Custom Code block doesn't get validated, so you could include something like this:
<div id="test" style="background: -webkit-linear-gradient(top, #2F2727, #1a82f7);
background: -moz-linear-gradient(top, #2F2727, #1a82f7);"/>