While @Kjetil is of course right that there is nothing special about s.e.s in a dummy variable regression, it may be instructive to look at how the expressions look like explicitly.
Take the model (which slightly differs from yours in that there is a full set of dummies rather than an intercept and dummies for all but one category)
$$
y_i=\beta_1D_{1i}+\beta_2D_{2i}+u_i
$$
where the dummies are such that $D_{1i}+D_{2i}=1$ for all $i=1,\ldots,n$.
Let there be $n_1$ observations such that $D_{1i}=1$ and $n_2$ such that $D_{2i}=1$. Then, the formula for the variance of the regression coefficients, $\sigma^2(X'X)^{-1}$, simplifies to
$$
Var(\hat\beta)=\begin{pmatrix}\sigma^2/n_1&0\\0&\sigma^2/n_2\end{pmatrix},
$$
which are indeed nothing but the respective variances of the sample means of the $y_i$ belonging to the two different groups. The off-diagonal entries must be zero as the second regressor always has a zero entry when the first has a unit entry, so when computing the off-diagonal entries of $X'X$, we must multiply zeros and ones.
When we have one unit column and one dummy (here, $D_{1i}$), $X'X$ will become
$$
\begin{pmatrix}n&n_1\\n_1&n_1\end{pmatrix}
$$
so that
$$
(X'X)^{-1}=\frac{1}{nn_1-n_1^2}\begin{pmatrix}n_1&-n_1\\-n_1&n\end{pmatrix}
$$
or
$$
(X'X)^{-1}=\begin{pmatrix}\frac{1}{n_2}&-\frac{1}{n_2}\\-\frac{1}{n_2}&\frac{n}{nn_1-n_1^2}\end{pmatrix}
$$
Hence, the off-diagonal is no longer zero, but basically cancels out the variance of the baseline category. I am not so sure what to make of this finding, but note that this implies that the variance of the sum of coefficients in the regression with intercept,
$$
Var(\hat\beta_0+\hat\beta_1)=\frac{1}{n-n_1}-2\frac{1}{n-n_1}+\frac{n}{nn_1-n_1^2},
$$
equals the variance of $D_{1i}$, $1/n_1$, in the regression with two dummies.
Here is a little numerical illustration of these ideas.
n <- 1000
y <- rnorm(n) # some dependent variable
x1 <- rbinom(n, size=1, p=.4) # a dummy regressor
x2 <- 1-x1 # its complement
(reg1 <- summary(lm(y~x1+x2-1)))# the regression with full dummies
n1 <- length(y[x1==1]) # the y's belonging to the first regressor
n2 <- length(y[x2==1]) # the y's belonging to the second regressor
mean(y[x1==1]) # the means are indeed the point estimates
mean(y[x1==0])
reg1$sigma*sqrt(1/n1) # reproduces the standard errors
reg1$sigma*sqrt(1/n2)
sd(y[x1==1])*sqrt(1/n1) # not exactly the same because the regression uses a "pooled" estimator for sigma^2_u
vcov(reg1) # off-diagonal element is zero
(reg2 <- summary(lm(y~x1))) # point estimate of the baseline category unaffected, also its standard error, but that of remaining dummy has changed
vcov(reg2) # now, the off-diagonal entry is no longer zero
sqrt(diag(vcov(reg2))) # another way to look at standard errors