Yes, that's how it works. Money that you take out of your IRA is generally money on which you have not yet paid taxes, so that money is subject to taxation when you take it out. Certainly your tax rate is not 100%, so not all of the money you take out is going to taxes.
You must think of a tax-deferred retirement account as being partially your money and partially the government's money in proportion to your marginal tax rate, so when you take money out the government gets their proportional share. By incurring a large balance due that must be paid the following year you are simply keeping the government's share a bit longer than if you had given it to the government in the same year as the distribution.
To avoid having a large balance due to pay the following year you could have taxes withheld (10% or more) from the IRA distribution, reducing the amount that you would need to take out the next year. Depending on you tax situation you might find it beneficial to take out more in one year that you actually need for that year and less the next year, such as when the taxable amount of Social Security income depends on your AGI.
