First off, is it more accurate to refer to them as vassal or subject states, seeing as though in reality, that's what they were? They had no choice in their "alliance" with Rome (as Capua would prove in the Second Punic War) and were obligated to provide Rome with soldiers for their armies. Is it correct to, nowadays, refer to those cities as Rome's subjects?
As a second question, and the one posed in the title, why were they called allies? Obviously, the term is much friendlier than "subject" or "vassal", but was it really fooling anyone? Also, it wasn't like the idea of conquering cities via war and annexing them into your empire was completely unheard of. Or perhaps it was because of the previous rulers of the Italian peninsula; the leagues of Etruscans and Latins, or the various isolated Greek city-states, or the united (is it correct to call them united?) bands of nomads.
To begin, the Latin word that is translated "allies" is socii, so maybe we could consider using a less equal word for the translation. More important, socii was not the only word Romans used to describe their relationship with other cities. Amici (friends) and clientes (clients) were also very common ways to describe foreign relations and all three had different connotations. In addition, Romans had several forms of treaties they would sign with partners or defeated peoples which allowed those places varying degrees of autonomy.
The most important issue is how Rome conceived of the relationship, and it is similar to the way ancient people conceived of personal relationships. Every action was reciprocal. If Rome provided your city with protection, you should return the favor with man-power. If Rome gave you your gods back after you surrendered, you need to offer your obedience in exchange. If you helped Rome in a conflict, you could expect protection. Basically, Roman diplomacy was all about establishing a base of favors owed to Rome that the city could call on in need.
For a more in-depth view on the topic check out Friendship and Empire by Paul Burton. To look at the pressure of the Socii check out Fronda's Between Rome and Carthage.