Weighing by difference
Although there are several sources of weighing error that would be minimized by using the weighing by difference method (as discussed in the comments), I want to illustrate what I see as the limiting problem, that of the relative uncertainty of the measurement, which roughly scales (no pun intended, really) with the mass being measured.

Lets use a bit of an exaggerated situation for illustration. In particular, we'll say that we have one balance that can measure down to $\pu{0.001g}$, and can handle up to $\pu{100g}$ total mass. In reality you would likely have a high-mass balance for weighing directly into the beaker, or a low-mass balance for using the weighing boat. We are just using one really good balance to simplify this illustration, but the concept is the same either way.  

Lets say our beaker has a mass of $\pu{50g}$, our weighing boat is $\pu{1g}$, and we are to measure out $\pu{1g}$ of material. 

The beaker plus the material to be measured will then have a measured mass of ~$\pu{51.00 +/- 0.05g}$. This means that the relative uncertainty in the measured mass of the material is no better than $\pu{5\%}$($\pu{0.05g}$ out of $\pu{1g}$).  

The weighing boat plus the material to be measured out will have a measured mass of ~$\pu{2.000 +/- 0.002g}$. This means that the relative uncertainty in the measured mass of the material is $\pu{0.2\%}$ ($\pu{0.002g}$ out of $\pu{1g}$).  

So, even with two measurements rather than one, using the weighing boat method results in much less total uncertainty in the measured mass of your material as compared to weighing a small quantity of material directly into a large beaker.