Update: The current version of this answer is more intuitive (IMHO) than the previous one. See also this similar answer to a similar question.
The generalization of this problem to $n$ pieces is discussed extensively in David and Nagaraja's Order Statistics (pp. 133-135, and p. 153).
If $X_1, X_2, \ldots, X_{n-1}$ denote the positions on the rope where the cuts are made, let $V_i = X_i - X_{i-1}$, where $X_0 = 0$ and $X_n = 1$. So the $V_i$'s are the lengths of the pieces of rope.
The key idea is that the probability that any particular $k$ of the $V_i$'s simultaneously have lengths longer than $c_1, c_2, \ldots, c_k$, respectively (where $\sum_{i=1}^k c_i \leq 1$), is $$(1-c_1-c_2-\ldots-c_k)^{n-1}.$$ This is proved formally in David and Nagaraja's Order Statistics, p. 135. Intuitively, the idea is that in order to have pieces of size at least $c_1, c_2, \ldots, c_k$, all $n-1$ of the cuts have to occur in intervals of the rope of total length $1 - c_1 - c_2 - \ldots - c_k$. For example, $P(V_1 > c_1)$ is the probability that all $n-1$ cuts occur in the interval $(c_1, 1]$, which, since the cuts are randomly distributed in $[0,1]$, is $(1-c_1)^{n-1}$.
If $V_{(1)}$ denotes the shortest piece of rope, then for $x \leq \frac{1}{n}$, (following Raskolnikov's comment) $$P(V_{(1)} > x) = P(V_1 > x, V_2 > x, \ldots, V_n > x) = (1 - nx)^{n-1}.$$
Therefore,
$$E[V_{(1)}] = \int_0^{\infty} P(V_{(1)} > x) dx = \int_0^{1/n} (1-nx)^{n-1} dx = \frac{1}{n^2}.$$
David and Nagaraja also give the formula Yuval Filmus mentions (as Problem 6.4.2):
$$E[V_{(r)}] = \frac{1}{n} \sum_{j=1}^r \frac{1}{n-j+1}.$$