Lara and I went down south reaching Morondava first and Toliara after. We were a girl and a boy on two bikes. We never ever had the impression to be in an unsafe place or to be in danger. In one occasion we also ride for over two hours in the dark between Antsirabe and Ambositra to reach the the destination.
Obviously it is a very very rural conuntry with no facilities outside big or busy towns. There is no electricity outside big towns and people tend to drink a lot. It is very easy to find drunk man hanging around at night.
I guess you only need to plan ahead the night before which will be your next destination knowing that there won't be any intermidiate stop. Make sure you can make it and don't forget that there are stretch of 300km without petrol stations.
Madagascar is a beautiful country.
Don't miss the fishing village on the coast around Morondava. Isalo Park it is unbeliaveble beautiful. It looks like a T-Rex will suddently appear from behind the mountain. On the opposite just a day riding away Ranomafana Park is a tropical jungle! Fantastic.