The initial intentions for this filing method was for separating and divorcing spouses who were not willing to file their taxes together. However, there are other reasons people find this filing method beneficial.
One uncommon yet key reason married people file separately is if they suspect their spouse has been involved with tax fraud or evasion (currently or in the past). Filing separately will allow the innocent spouse to avoid any potential tax liability. There are other ways to avoid tax liability than filing separately if the liability isn't as serious as tax evasion. Consult with your tax preparer for these methods.
Even a happily married couple can benefit when filing separately.
The main reason people chose to and benefit from filing separate is in a childless marriage when one spouse has a higher income while the other spouse has substantial potential for itemized deductions. For example, if one spouse has a lot of medical bills and a low income, this partner will likely meet the threshold required to be able to deduct these medical expenses on their tax returns. The partner with the higher income will have a higher threshold to start deducting these expenses and filing jointly will eliminate the chance for the lower income spouse to claim these deductions.
It must be noted that when married filing separately, both spouses must choose the same method of recording deductions. So if one spouse itemizes their deductions, the other spouse must do so as well even if their standard deductions are higher and will result in a greater return. In some cases, this can be seen as a con to filing separately. Some other limitations include the inability to claim the following: Earned Income Credit, Child Tax Credit, Child and Dependent Care Credit, Student loan interest deduction, any type of education credit, and elderly/disabled credit.
There are a lot of factors that goes into married filing separately. If the couple is unsure, it may be best to calculate the return both ways to see what will result in a lower tax bill. In general, couples with no dependents or no education expenses can benefit under certain situations. As always, consult with your tax preparer if you have questions.