The title really says it all. Since "you" can be singular or plural, why don't we say, "You is" when using "you" as singular? We say "he is" or "they are". Why is it different?
There are two answers to this.
The simplest is that "are" is the form of "to be" used for first person plural, third person plural, and both plural and singular in second person (with you). Thus, "are" with a singular "you" is also singular. It just looks exactly like the plural form. The same goes for "were" in the past tense, or for any other verb in second person: The form of the singular is identical to that of the plural.
The other answer is that "you" is always plural. Or at least, it was so historically, and that has carried over into the present in verb conjugation. Formerly, English had two separate second person pronouns: "thou" and "ye". "Thou" became increasingly intimate, and then increasingly archaic, and finally died out altogether. Meanwhile the plural nominative (subject) form "ye" was replaced in all uses by "you", formerly limited to objective uses. Since ye/you were plural, they always took a plural verb. Now in the present case, we can use "you" as either singular or plural, but it still always takes a plural verb, as it has always done.
It should also be noted that even when "thou" was the singular form, the second person singular of the verb was not identical to third person singular, but rather:
"he is" vs. "thou art"
"he builds" vs "thou buildest"
"he was famished" vs. "thou wast famished"
Actually, the English verb to be has "lost" the form for the second person singular and uses the plural form "you are" also as a substitute for the second person singular.
A table of the forms of to be should be in this form:
1st pers. am are
2nd pers. --- are
3rd pers. is are
Remark The second person plural is also used for the second person singular, if you want to see it this way. But you can also say in English everybody, even a single person, is addressed in a respectful way as if the person were several persons.
If you are interested in the historical process of this development you'll find information in en.wikipedia under "you".
The form that fell into disuse was "thou art". The King James version of the Bible still uses this and other old forms. Example psalm 63: