While smaller populations do have smaller standard deviation than large ones, they have larger percentage standard deviations.
You can consider the number of successes as the sum of independent random variables $$ N = X_1+X_2+\ldots +X_n$$ where each $X_i=1$ if the $i$-th trial is a success and $X_i=0$ if it is a failure. The mean number is of course $$E(N) = nE(X) = np$$ where $p$ is the probability of success. For independent variables, the variance adds as well $$ \mathrm{Var}(N) = n\mathrm{Var}(X) = np(1-p).$$
So, as you said, the standard deviation is larger for larger samples and in fact increases proportional to $\sqrt{n}.$
However, when you look at a question like the one you started with: what is the probability of having more than $60\%$ successes, you aren't interested in the standard deviation, you are interest in the standard deviation relative to $n.$ So this is $\sqrt{\mathrm{Var}}(N)/n$ which is proportional to $1/\sqrt{n}$ which goes down with $n$ (in other words the size of percentage fluctuations, not absolute fluctuations). This is why there is a higher likelihood of more than $60\%$ successes for small samples when $p=.56$.
The intuitive reason for why the percentage fluctuations go down with $n$ is that as you you take a larger and larger sample you expect your true percentage of success to be very close to its long run average (things tend to average out to their true means... this is the law of large numbers). In other words the width of the distribution approaches zero.
The intuitive reason why your standard deviation goes up as $n$ increases is that there are more possible combinations of successes and failures as $n$ increases, and even though they tend to cancel out toward the mean, the amount by which they miss the mean increases with $n$. For $1000$ trials with $p=.5$ so that the mean is $500$, it could over or undershoot the mean by up to $500$ whereas for $10$ trials it could only over/undershoot by $5.$ Now, it's very rare for it to overshoot by that much, particularly in the $n=1000$ case, so things are a bit more complicated than this, but it's still true that the distribution is wider by a factor of $10$ in the case with $n=1000$ compared to $n=10.$