Recently I saw a review of a book, (Muslims in Indian Cities- Tragectories of Marginalization, ed. by Christophe Jaffrelot and Laurent Gayer, 2012, Harper Collins), by Hassan Javid, a LUMS Prof. in a daily newspaper of Pakistan (http://www.dawn.com/news/1084234).
I am currently reading this book, and all the articles based on solid ethnographic details are very well written. But, as an academic working on Muslims, I also know that I cannot say that this is the case or the only reason, all over India.
I have been working on Shahjahanabad/ Old Delhi, and did my PhD on Segregation of Muslims in this part of Delhi. It is a reality, no doubt, but to break down all the complex processes involved to just one aspect is being too simplistic and to mention it as a vindication of 'Two- nation theory' debate, would be immature.
I have interviewed people, and having spent most of my life in Shahjahanabad, I also know that people want to live here, not only because they are insecure or fear for their lives but because they choose to (come on, in todays' time? When a Punjabi locality like Lajpat Nagar is being inhabited by Afghanis, Kashmiris and other Muslims) .
Old Delhi walas like the cultural, social environment of Shahjahanabad. It makes economic sense too, as most of them are self- employed in this area, so would like to stay near their karkhanas/ shops, and as cost of living or average expense of living here, is cheap as compared to other parts of Delhi, i.e. food, rent, etc.
It may lack the greenery or the infrastructure, but people still continue to live in Shahjahanabad, to enjoy the social joys that living with the community offers. Just like Bengalis like to stay in Chittranjan Park, or Punjabis in Jangpura/ Rajouri Garden/ Shalimar Bagh, etc. and these localities are not termed as 'ghettos'. I have reservations against people branding, Shahjahanabad as a 'Muslim ghetto'. There are a lot of Hindu families, as there are some Sikhs and Christians too, who still live in many areas of Old Delhi, side by side with Muslims.
Ghettos are formed by migrants, Shahjahan built this city in 16th century for all his subjects in the 16th century. Some families have been living here since generations, and find it hard to even imagine a life beyond the walls of the Old City. If you ask them, they are not 'marginalized'(heavy word!), but have very few options of areas which would also suit their pockets, and would give them a 'comfortable environment' where they would be free to practice their religion too!