The "freely" isn't a very well defined term is it?
What it is supposed to be saying is that the neutrinos "mostly" pass freely through matter but not quite completely.
There is a measurement called the "cross section". It tells you how likely it is that one particle will "run into another". It is just like it sounds a kinda measure of how big it is. You know the old saying "as big as a barn door". Well that suggests that a barn door has a very large cross section and would be hard to miss.
A neutrino passing through other matter has a very small cross section, very, very, very, very small but not zero. If you fire enough neutrinos throughs a big enough chunk of matter then one neutrino in a few kajillion will actually hit something. (Hit meaning interact with).
from
http://zebu.uoregon.edu/~imamura/208/feb3/results.html
"10**10 neutrinos per square centimeter per second at the Earth. "
And with those passing through a giant tank of water 10's of meters on a side you get a few collisions (very few).
So to say they pass "freely" is true but it is not true that they NEVER interact.