I think we should begin by shedding lights on some aspects:
The Inquisition wasn't a monolithic entity. There were different - and fairly independent - branches of it, the most notorious of which was the Spanish Inquisition (founded in 1478). There was also the Congregazione della Sacra Romana e Universale Inquisizione... the Roman Inquisition, that is, whose jurisdiction applied to most states of the Italian peninsula (except for Lucca, Florence and Venice - which had its own system); interestingly enough it was established much later than its Spanish counterpart, in 1542.
The Inquisition, or at least its Roman branch, was quite different from what we tend to think of it today; it was basically an organisation tasked with censorship, which was done through the Index Librorum Prohibitorum - a list whose books/essays/treaties were found to be in contrast with the Church's doctrine. In order for you to publish your work, you had to apply for - and be granted - the imprimatur first (the bureau's authorisation to print) and only then you were allowed to publish it: the books that didn't meet the criteria or were smuggled... these were usually Protestant treatises... were requisitioned and burned, and the clandestine printers (if there were any in the country), jailed.
As far as its reputedly fearsome Tribunal was concerned, the defendant - whose writings got the author in trouble, having caught the eye of the censors - usually had the right to defend him/herself in court and to summon witnesses in his/her defence; in this respect, the trials were remarkably fair for the time. Also, people rarely underwent torture and executions (not always by means of burning) happened even more seldom; authors like Giordano Bruno was an exception, rather than the rule.
Who did the Roman Inquisition burn then? If you - like Bruno - had espoused heretical beliefs (which in his case were hardly Christian), published them without the Bureau's approval and refused more than once to repudiate them... mocking the jury in the process as he did, well, then you may have been dealt with. I'm not justifying their means but capital punishments were carried out rather seldom and before getting to that point, you would have been given the possibility to defend yourself in a relatively fair trial.
Who did the Spanish Inquisition target? The two organisations had different goals and unlike its Roman counterpart - more focused on censorhip - the Spanish/Portuguese branches mainly targeted conversos (Jews who had been forced to convert to Catholicism) and moriscos (former Muslims - not necessarily Arabs or Berbers!) simply because many of them were deemed to be 'false converts' and thus 'untrustworthy'. Admittedly, its methods were a tad worse than those employed by its Italian counterpart but still...
Who was responsible for the deaths of 'the witches'/unrepentant Protestants elsewhere? The magistrates operating in the various Italian, and European, states of the time: the secular authorities... here's who.
How many died at the hands of the Inquisition, Roman and not? Historians do not agree over the exact number, but some 100,000 trials took place all over Europe throughout the centuries, and some 40,000 defendants were put to death.
Also, Protestants were in many cases much more harsher towards non-conformists than the Inquisition(s) ever were. Much of today's stereotypes about such organisations come from 18th/19th-century works of literature, whose authors took - more often than not - an anti-clerical (or at least anti-Catholic) stance.
Finally, I believe we should note how the (various) Inquisition(s) often acted under the direct orders of the rulers of the country they were based in, rather than to the Pope in Rome.
If you'd like to read more about it, I'd suggest reading Henry Kamen's The Spanish Inquisition: A Historical Revision.