As long as the governing body of these Madrassas are providing adequate schooling without any indoctrination of intolerant or extremist behavior, then they should not be a problem at all. Infact, Madrassa's can be a effectively used to educate our burgeoning young populace.
Madrassas are basically schools, and with the right curriculum and progressive teachers, it could be a great source of education for poorer classes. This is where the government could come in and facilitate access for Madrassa's to a better curriculum, one that concentrates on the positive aspects of education and our religion itself.