There are many kinds of universal hashing, many of which are not based on polynomial evaluation.
However, the most common kinds of universal hashing, i.e. those which are used for computing message authentication codes (MAC) in the TLS and SSH protocols (using poly1305 or GCM), are based on polynomial evaluation, where the message is the sequence of coefficients of the polynomial and the secret key of the MAC is the value at which the polynomial is evaluated.
The polynomial corresponding to a MAC is evaluated only once at the sender and once at the receiver, usually in a single pass over the data, simultaneously with its encryption or decryption. Frequently the reading or writing of the data from/to the main memory limits the throughput of the MAC computation (caches do not help, because the data is not reused), in which case a better algorithm than Horner cannot provide significant speed-ups.
Besides their application in MACs, which is ubiquitous now in Internet communication, I consider the other applications of universal hashing as minor, because the "universality" property of such hashes seldom provides any substantial benefit over alternative hash functions that do not have this property, but which guarantee other more useful properties. (The "universality" property is just a statistical property of a family of hash functions, while instantiated universal hashes may happen to be quite bad hash functions. For instance, in AES-GCM it is possible to choose by bad luck a secret key for which some reordered messages have the same hash value with the original message, so tampering with the message remains undetected. Fortunately, the adversary cannot guess when the sender has chosen a bad secret key, in order to try to alter the message.)