Ciao Neha,
The one day tour you've linked to has the benefit of you not having to worry about transportation and when time is limited, they take you from Florence to Siena, you spend the morning there and then head out of Siena into Chianti to stop at a winery where you do both wine tasting and lunch.
Then you stop in San Gimignano for an hour or two, then head on to Pisa.
You have some time at each place, but as you can imagine it just a few hours... so the pace is quick.
When you have a day or two to see all of Tuscany and want to see the highlights, I do recommend this tour, even if you don't get to spend too much time at each place.
Personally, if you have the time and you're traveling with kids, I wouldn't recommend it.
First, if you have the time, all of Tuscany and Italy for that matter is best experienced without being in a hurry. Take your time to explore, even if you never step foot in any museum. All of the towns are museums in their own right, with all of the beautiful palaces, piazzas, statues and monuments everywhere. You want to take time over meals, and enjoy lots of gelato as you walk around! ;-)
Then, with children, if they get tired and want to take a break (and enjoy a gelato, for example) or go head back "home", you don't have control over your schedule in this type of tour. A 12 hour day is long.
If Florence is your base, I'd do a day trip to Pisa and Lucca (they are close to each other, you can do half a day in each), then a day in Siena and the rest of the time in Florence! There is plenty to see and do at each.