Because Basque is not an Indo-European language. Most modern experts either argue that Basque is a language isolate, completely unrelated to any other known language on earth, or that it has distant, ancient "genetic" relations to other far-flung or now-extinct language trees. Vennemann, for instance, argued that Basque is the last-surviving member of a much larger European "Vasconic" language tree. Some have tried to connect it with a larger "ancient Iberian" language tree, and others point to possible links further afield (Ligurian, Georgian, etc). The evidence available for Basque before a few hundred years ago, especially inscriptional evidence, is extremely poor, which makes all of these arguments very difficult for historical linguists. The current dominant hypothesis is that Basque was being spoken, in its ancient form, in northern Iberia in the millennia preceding the arrival of the Indo-Europeans into western Europe, the Celts and Celt-Iberians in particular. It is probably an accidental survivor of a much larger system of pre-Indo-European languages stretching back into the Neolithic, virtually all of which are long gone with no evidence of their existence.
Forni has recently attempted to link Basque to Indo-European, but most reject his arguments. Very recently, Blevins has a go at it as well. Blevins is the most up-to-date book on the topic, as far as I know:
Blevins 2018, Advances in Proto-Basque reconstruction with evidence for the Proto-Indo-European-Euskarian hypothesis (Routledge).
/u/Rmnclnggs already gave a good answer, but I'd like to contribute some info on how historical linguists work and why Basque isn't very useful for them.
The heart of historical linguistics is the comparative method. It's quite simple: you start out by comparing two languages and looking for correspondences. The most important correspondences are sound correspondences in the basic vocabulary. For example, the German translations of the English words think, thin and thorn are denken, dünn and Dorn – they're all very similar to the English words, but they start with d where the English words start with th. In other words, there's a correspondence between English th and German d.Sometimes correspondences can be due to loanwords, onomatopoeia (words that imitate natural sounds) or chance. But sometimes the correspondences between two languages are so systematic and so extensive that these explanations aren't sufficient. In those cases,the correspondences must be due to a common origin, a shared ancestral language (the technical term is protolanguage) that both languages evolved from. This is how we know that the Indo-European (IE) family of languages exists: there are systematic and extensive correspondences between the IE languages, so we know that they descend from a common protolanguage, and we call that language Proto-Indo-European.
But the comparative method doesn't just tell us that protolanguages like Proto-Indo-European existed. It also allows us to reconstruct those languages to a greater or lesser extent. For example, as you may know, English and German are part of the Germanic family (the group of languages descended from Proto-Germanic, which in turn is a descendant of Proto-Indo-European). By looking at sound correspondences such as the th/d correspondence above and its equivalents in other Germanic languages, we can make an educated guess at the Proto-Germanic sound that this correspondence originated from. In this case, taking into account all the available evidence, historical linguists believe that the original sound was *þ (pronounced like English th in words such as think), which still survives in English but was simplified to d in languages such as German. And by combining all the relevant sound correspondences, entire words in the protolanguage can be reconstructed. The Proto-Germanic forms of the three words given above have been reconstructed as *þankjan, *þunwi- and *þurnu-, for example. (The asterisk indicates that a sound or word has been reconstructed.)
The comparative method isn’t the only tool of historical linguists. There are other methods which don’t require knowledge of several related languages. For example, you can trace the exchange of loanwords between languages, which can tell you a lot about the geographical position of different languages at different points in time or about the relationship between their speakers. Another example is internal reconstruction, where irregularities in a language can be used to deduce information about an earlier stage of the language. But the comparative method is crucial. If you want to study the exchange of loanwords in the distant past, for example, you probably won’t get far unless you can reconstruct the protolanguages that were spoken back then.Now you probably see why Basque isn’t very informative for historical linguistics: it’s just one language. The comparative method can be applied to the different Basque dialects, but that only gets you to the common ancestor of these dialects, which may be called Proto-Basque. You still don't know about other languages that were spoken at the same time as Proto-Basque.
They can’t because pre-ie Europe was probably really linguistically diverse, we shouldn’t see “pre-ie” as a language family like Afro-Asiatic or Indo-European, so there is no certainty that a pre-ie language might be related to Basque. We know several pre-ie languages from writings and substrates but they don’t seem to be related at all and there were probably several language family, some pre-ie language families we know about are:
-Tyrsenian: Rhaetian, Etruscan and Lemnian.
-Vasconic: Basque, Aquitanian
There have been attempts to connect several languages to Basque but with varying degrees of success, such languages are:
-Iberian (it might have had similar case endings and numerals to Basque)
-Pre-Celtic (possible cognates)
-Nuraghic (possible cognates)
-Minoan (as far as I know every attempt at relating Basque to the ancient language of Crete was a failure)