That depends on your definition of discrimination and poor treatment. Just as well, the time period you're referring to.

Being a heavily bureaucratic empire, the Ottomans had a classification for Christians and Jews; they were referred to as dhimmis, meaning they were "People of the Book." This classification was applied to laws and taxes throughout the empire in different ways. While Muslim subjects paid a tithing tax related to the pillars of Islam, the dhimmis would pay a poll tax called the jizya. This tax was a little higher than those Muslims would pay, and the forms of payment were considered demeaning in a lot of ways. There are accounts of local tax collectors making them walk (as opposed to using horses, carts, mules, camels, etc) to pay their taxes, that they must dress in different types of clothing, and that when physically paying the tax, their hands must be on the bottom to show subservience of a sort. While I have not seen any verification of such claims, these laws were often attributed to attempts to make Christians and Jews convert to Islam.

Towards the 15th and 16th centuries, this was curbed to an extent. Taxes were still more heavily applied, but changes were made within the legal system and the religious system to make the empire seem more tolerant (as European powers began to pose more of a threat to the Ottomans, but that's a different issue). Namely, Suleiman I (1520-1566) reformed Islam to the Hanafi School, which of the four major schools of Islam is the most tolerant towards non-Muslims and non-Arabs. This was in part to reestablish power as Turkic Muslims and to solidify the Ottoman claim to being a multiethnic, multiconfessional, polyglot (several languages) empire.

However, in this period the Devsirme became an important part of Ottoman military and bureaucracy. The Christian/European provinces (modern Greece and Bulgaria mostly) would pay a human tax of young boys who would be taken to the capital and be given what was possibly one of the best educations at the time. Depending on whether they were intellectually or physically proficient, they would either become political bureaucrats or join the elite Janissary corps. Most contemporary Turkish sources claim that this was not just good for the empire, but, good for the young men who were taken away from their families at young ages. Most recent Bulgarian and Greek sources see this as nothing more than slavery, so, take it as you will.

In the later centuries of the Ottoman Empire (Possibly earlier, I'm a bit rusty and no longer have my books, so forgive me) they instituted a judicial system called the Millet system. While before, everybody would be tried by Shariah (Islamic) law, Christians and Jews would be judged by their own respective religious law regarding religious matters. This was only true to the extent that no Muslims were involved in the matter; in those cases, Shariah took precedence over all else. Also, non-Muslims of any kind were not allowed to testify against Muslims within any court, which caused obvious judicial issues.

I wrote a paper a few years ago on this that covers most of this more in depth, or at least more coherently. If you'd like to read it, just send me a message. Otherwise, I apologize for any errors in spelling or coherency, I'm running on caffeine at the moment.

Sources:

Franke, Patrick. “Minorities: Dhimmis,” In Encyclopedia of Islam and the Muslim World. Edited by Richard C. Martin, 451-452. New York: Micmillan Reference

Schmuelevitz, Aryeh. The Jews of the Ottoman Empire in the Late Fifteenth and Sixteenth Centuries. Leiden, The Netherlands: E. J. Brll, 1984.

Lewis, Bernard. The Jews of Islam. Princeton: Princeton University Press, 1984.

(While Jewish accounts were more heavily documented, most of the same applied to Christian subjects as well.)