Modern automatics have come a long way through research, development and improvements in technology to become just as reliable as manuals if not more so. They are barely any more expensive to buy, and offer the potential for better fuel economy/refinement - especially for motorway driving due to additional ratios (anyone rocking an 8/9 speed manual?)
My Octavia VRS is a DSG and it's great, I'd even go as far as saying I enjoy it. It's great during daily commuting in traffic, but it's also great when "on it" because of the way it shifts so quickly that there is almost no break in acceleration. People will argue it's less involving, but it's hardly the most engaging to start with and the benefits outweigh the slight loss of involvement.
Fun weekend sports car that you'd actually drive for the sake of enjoyment = manual all day long.
Daily driver for commuting and family transport = auto all day long.