You can absolutely use Whooo's Reading with your children in a home environment. The program will work the same way as it does in a classroom; you simply create a "teacher" account at www.whooosreading.org (any email address will work, it does not have to be a school-issued email address).
Once your account is created, add your children as "students" on the Roster page (when it asks you to input a school, simply enter "Home" or "Homeschool" as the school name).
Finally, give the kids their login information to access their own accounts. They can then use Whooo's Reading to assess their reading comprehension at home.