FigTree is my favorite too. But it is a graphical viewer for viewing the phylogenetic trees. My need here is a tree file in Newick format, which is void of bootstrap information in it. Repeating the analysis is also not a feasible task as it is a big data set and it takes more than a week's time in a cluster computer to complete the run.
My favorite program, Seaview, was designed by French colleagues...
If you don't want to rerun the analyse, you can always remove the bootstrap values in your tree files using the egrep function or in your figure file using an image editors...
There are plenty of tricks when it comes to communicate about phylogenetic results.
If you decide to run again the analysis, you can use DARwin6 software. You can find it using google and it is free. You have many options. You can add bootstrap values of not. You can also use different colors for your populations or sub populations...