It’s a classic case of Photoshop versus website. Existing wireframing and prototyping tools are incapable of accurately reflecting the environment of the web.
They produce static designs that can’t be seen through the variable known as the web browser. And when you build the final website, some elements won’t look exactly like their draft counterparts, and the client will notice those minor differences in fonts, positioning, etc.
You may be more comfortable with a graphics program, and rendering the design iterations may seem to take longer if you have to hand-code the HTML.
However, the advantages of creating a wireframe in HTML from the start are beginning to outweigh the alternatives: not only do we have new layout elements in HTML5 and more powerful selectors and styling in CSS3, but by combining them, we can throw together a simple layout quickly.