Let $p:\mathbb{R}\rightarrow S^1$ be the usual covering map, $p(t) = e^{it}$.
Claim: For every continuous homomorphism $f:\mathbb{R}\rightarrow S^1$, there is a continuous homomorphism $\tilde{f}:\mathbb{R}\rightarrow \mathbb{R}$ for which $f = p\circ \tilde{f}$.
Proof: Let $f:\mathbb{R}\rightarrow S^1$ be any continuous group homomorphism. By the path lifting property of covering spaces, there is a unique lift $\tilde{f}:\mathbb{R}\rightarrow\mathbb{R}$ with $\tilde{f}(0) = 0$ and $p\circ \tilde{f} = f$.
Further, $\tilde{f}$ is a homomorphism. To see this, note the map $\mathbb{R}^2 \ni (x,y)\rightarrow f(x+y)$ has two lifts $\tilde{f}(x+y)$ and $\tilde{f}(x)\tilde{f}(y)$. Since both of these lifts map $0$ to $0$, they must agree everywhere.
$\square$
To summarize, for each continuous homomorphsim $f:\mathbb{R}\rightarrow S^1$, we can factor $f$ as $p\circ \tilde{f}$ where $p$ is the standard homomorphism and $\tilde{f}:\mathbb{R}\rightarrow \mathbb{R}$ is a continuous homomorphism of $\mathbb{R}$.
Thus, we have reduced the classification problem to classifying continuous homomorphisms from $\mathbb{R}\rightarrow \mathbb{R}$.
Claim: Every continuous homomorphism $g:\mathbb{R}\rightarrow \mathbb{R}$ is of the form $g(t) = rt$ for some $r\in \mathbb{R}$.
Proof: Set $r = g(1)$. Since $g$ is a homomorphism, $g(n) = rn$ for each $n\in \mathbb{Z}$. Further, for the rational number $\frac{1}{n}$, we have $r = g(1) = g\left(\underbrace{\frac{1}{n} + ... + \frac{1}{n}}_{n \text{times}}\right) = \underbrace{g\left(\frac{1}{n}\right) + ... + g\left(\frac{1}{n}\right)}_{n \text{times}} = n g\left(\frac{1}{n}\right)$, so $g\left(\frac{1}{n}\right) = r\frac{1}{n}$.
Thus, $g(t) = rt$ for any rational $t$. Finally, by continuity of $g$, $g(t) = rt$ for all real numbers $t$.
$\square$
Combining these two claims, we have $f(t) = e^{irt}$, as claimed.