All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad is His slave and Messenger.
If you do not sell cigarettes in the cafe and you only sell permissible food and drinks, then it is permissible for you to do so and you are not sinful. The fact that you do not object to the customers when they smoke in the cafe does not affect your income from it. However, it is more appropriate for you and for all the people who have shops to forbid smoking in their premises as this is changing wrong and repelling evil, and forbidding causing harm to people.
As regards not performing congregational prayer because of the cafe, then this is not permissible if this is always the case; rather, you are obligated to attend the congregational prayer even if this leads to closing the cafe during the period of the prayer. How could you hear the call to the prayer, the good and the success while you are immersed in this worldly life rejecting the call to the prayer; did you not hear the saying of Allaah (which means): {[Such niches are] in houses [i.e. mosques] which Allaah has ordered to be raised and that His name be mentioned [i.e. praised] therein; exalting Him within them in the morning and the evenings. [Are] men whom neither commerce nor sale distracts from the remembrance of Allaah and performance of prayer and giving of zakah. They fear a Day in which the hearts and eyes will [fearfully] turn about.} [Quran 24:37]?
So, don’t you wish to be among these people in the sense that your business would not divert you from the prayer and from the mention of Allaah, as there is no good in what diverts from them?
In any case, since you do not sell forbidden things and you wish to sell the shop, then it is permissible for you to benefit from its price. It is also permissible to keep it, but you should not miss the congregation and the performance of the prayer in the mosque.
Allaah Knows best.