But history had not been kind to the relations between the two communities. The 190 year long British period is known for Hindu Zamindar's collaboration with the British and economic oppression of the Muslims in Bengal. This has been the main reason why Bengal Muslims opted for Pakistan to escape that domination and oppression. West Pakistani's again took the role of oppressors during the 24 years of Pakistan period, so Bangladesh was born to achieve freedom from that oppression.
Most of the Hindu Zamindars and money lender families have left for India since 1947. The Hindu's that remain in Bangladesh I believe are mostly from economically backward classes and not the elite British collaborator families. Because they are from the minority community, they are targeted by powerful local people from the majority Muslim community, regardless of party affiliation. A Hindu family's property, mainly land, is a lucrative target as they can be bought at a fraction of the market price if the family is threatened and, as a result, have to leave for India for better security of life and property (Jaan and Mal, as the article in OP mentioned). This indeed is the main economic driver for the migration. Land is scarce commodity in this densely populated country, even rural land has high value. So no party in power can fully solve this problem, unless the economic condition improves, the country develops at a higher pace and law and order situation improves where life and property is secure for all people including those of minorities.