If the pikemen are advancing on your encampment, what will you do? Abandon your supply train?
The scenario is an imaginery one. By the time the enemy has reached your supply train he has not only chased off your cavalry, but fought his way past every other unit as well.
To have a supply train in every area occupied by cavalry would imply that the mobility of the cavalry was limited to the speed of a heavily laden horse-and-cart. That would defeat the whole object of having cavalry.
Really? Pikes weren't particularly effective vs infantry in post-Macedonian warfare. Too slow, too inflexible, too immobile. The Phalanx went out of style a long time ago. Weren't bit in Medieval periods except for some militias, and even then it was mostly as cavalry defense.
Pikes were used rather effectively against both infantry and cavalry. Also, pikemen were typically equipped with swords as well for close-quarter combat. Pikes were common weapons for a period that lasted from the 14th to the 17th century, and they were still in use in the 18th Century. It wasnt until the mid-17th century that muskets became the main weapon of choice against infantry.
http://en.wikipedia.org/wiki/Pike_(weapon)
http://militaryhistory.suite101.com/article.cfm/the_pike_as_a_weapon_in_history_
Bayonets are much shorter, and aren't used in formation at all.
They were very much used in formation, in infantry squares, to protect against cavalry charges. Here is a famous example:
http://www.uncp.edu/home/rwb/waterloo_001.JPG
And again, the gameplay issue (without a unit that can threaten cavalry, you don't have to be careful about your placement of them) stands unchallenged.
I really cant see what the problem is. Cavalry can be attacked by the same units that can attack cavalry in real life, including:
1. Other cavalry. (The most important method to deal with enemy cavalry.)
2. Archers.
3. Artillery.
4. Not forgetting, of course, elephants!
In Civ 4, Im always extremely careful about where I place my cavalry, but this isnt because I am terrified of rampaging pikemen.