Some history: the "Marriage Penalty" is political language applied after the fact. If you turn it around and look at it from the other end, it is a tax subsidy for people who are single.
Why would the government want to subsidize being single? Well, before 1969 the tax code considered a married couple to each be earning half of their total income, for purposes of tax. Because we have a progressive tax in the U.S., this meant that married couples with a combined income of $X would pay less tax than a single person earning $X, since the married couple's incomes considered individually as X/2 would fall into a lower tax bracket. So in 1969 they changed the law to try to compensate for this "singles penalty" by making the tax rates better for singles.
In fact, if you were thinking about human economic and social behavior in a sort of naive and old-fashioned way, a tax break for "single" people, ie: people living alone, makes a bit of sense anyway. Dual-income families enjoy economies of scale that single people do not: two people can share a refrigerator, the cable bill, a phone line, and so on. A single person has to do all of that on one income. Of course this is an oversimplification, for obvious reasons: single people find roommates, and married couples don't always have dual incomes. But in this light the marriage penalty is not totally unfair the way it is sometimes made out to be. As an extreme example, blind taxpayers are allowed a larger standard deduction, because of the hardships of not being sighted in a sighted world. Yet no one gets up in the senate and rails against the "sight penalty".
In any case, consider that if you have a progressive tax, and you let married couples combine their incomes in any sort of scheme, it will always be unfair to somebody, because of the way the combined income changes tax brackets. As the law is today, a couple where one person earns all the income has a tax advantage being married; it's only as their incomes become equal that it becomes a "penalty".