I'm not worried about the major markets (Silicon Valley and New York) but about the rest.
I am in Minneapolis and my resume has "founder" on it. I've had no problems finding employment. In my current job, it actually helped me get hired: my boss specifically wanted to assemble a team of entrepreneurially minded people. In my previous job, it didn't help but it didn't hurt either. So my personal anecdata says it's not a problem at all.