You might try contacting Experience Plus http://www.experienceplus.com
, who used to run a Pisa to Venice (and Venice to Pisa) bike tour (they may still do so, I just haven't checked for a long time). They may be willing to advise you as to specific places to stay.
In the smaller, quieter towns I'd have no concerns about security. In towns of, say, more than 10,000 population, I'd feel better if I could store my bike out of sight in the hotel, if not locked away. While not every establishment may welcome cyclists and bicycles, you should have no problem finding accomodations that do.
In Venice, I'd stay on the Lido island and take the vaporetto (water bus) into the main islands to sightsee. Wheeled vehicles are not allowed there, and in any case there are so many canals to cross over on bridges with stairs/steps that wheeling a bike around with you would be a big pain. And I'd definitely not leave a nice bike out of my sight in Venice, no matter how beefy a lock I had.