Robert Harvey's The War of All Wars gives a truly fantastic short history of the Revolutionary and Napoleonic Wars. His view is slightly Anglo-Centric, but extremely well-informed. In the book, he mentions an attempt by General Claude Malet to destroy the Napoleonic Government while he was in Russia.

But generally, you are correct; there was no organised, armed resistance to Napolenic rule, primarily because those opposed to the Government had been defeated in the Vendee (sp?), a bloody and fierce campaign in Northern France, at Toulouse (where Napoleon ironically earned his first major command), or fled abroad to become French emigrates, such as General Dumoriez and Carnot. Napoleon took over from the Directory, which spent a huge portion of time basically culling anyone opposed to their rule.

Many men, before and after Napoleon's reign, doubted his ability to rule. General Kleber, the military officer left in command in Egypt, thought him military incompetent and administratively foolish. But these were in the minority; Napoleon used the Army and the Police Force under Fouche to suppress dissidents, and kept these two groups happy by plying them with loots and riches from his conquests.

Plots were aplenty, but generally, no armed resistance movement occurred during his reign. I hope this helped.