The three things hurt Jericho
I should first start by saying that I loved Jericho and place it as my personal favorite TV show.
I think there are three main reasons why this show didn't find a larger audience and see's people dislike it:
1. Misconceptions with nuclear weapons. I find that many people associate any nuclear exchange with a total cold war nuclear war. I have even meet more then one person who believed that a single nuclear bomb would kill all life on earth. The realistic effects of small nuclear devices detonating in a dozen American city's probably went well over the heads of an audience whose only other nuclear viewing showed total nuclear war where thousands of HUGE bombs are set off.
2. A drama for men. In many ways I think that Jericho is a contradiction, it is a dialogue driven drama which focuses mostly on the masculine. Those who could mostly connect with the characters and plot would likely be easily turned off compared to Dexter, Mad Men or the other shows available at the time.
3. Series shows were on the way out. The Shields fifth season(arguable its best) saw a decline in viewership and almost all new shows presented stand alone shows within a series. Even Lost worked hard to have all of its episodes resonate with first time viewers. Breaking Bad and a couple other may have bucked the trend but I think the majority of shows were developed to appeal to jump in viewers and Jericho was not adapt to this type of viewership.