Okay, so this is a very interesting yet complicated question. However, it is one that should indeed be asked, as historical figures, even ones we might admire, make mistakes and should be held accountable for them. Disclaimer: I'm not a subscriber to the, "he was just a man of his time" apologia faction within American Civil War historiography, and believe we should critically engage historical figures in a way that takes the full scope of their actions (including social foresight) into account. I'm going to provide some context for Gen. Order 11, but this shouldn't be mistaken for an excusing of the words or implications of the General Order. Quick td;lr, Grant's order was seen as bad and unacceptably anti-Semitic at the time, and it obviously looks even worse today; however, there's more to the story than what one finds in the order itself.

So to make a VERY long story short, Ulysses and his dad, Jesse, didn't have what you might think of as a modern, loving father-son relationship. Their relationship throughout Ulysses' childhood and young adulthood seems to reflect a very strong, "I know what's best for you," vibe on behalf of the father. This was pretty par for the course during the mid-19th century, yet it's notable that Ulysses himself seemed to be a very compassionate, loving, and "present" father to his own children, perhaps as a response to his more clinical and business-like upbringing (Lincoln was similar in this regard). The point is, while Jesse seemed to care for Ulysses, in that he employed the young man when broke, sent him to West Point, etc., there wasn't a lot of give-and-take in the relationship. Ulysses did what he was told and had more of a "father" than a "dad."

Now, you're probably asking: what's this have to do with Gen. Order 11? Well, after U.S. Grant started climbing the military ladder during the Civil War, Jesse wasn't content to just sit back and enjoy his son's success from afar. No, Jesse had a lot invested in his son, and was eager to reap the rewards of his 40 year "speculation." Ulysses was a popular figure in the press in the early years of the war, and especially in Illinois and the mid-west, was comparable to a mid-level celebrity. By all accounts, Jesse had every intention of squeezing every possible benefit from this, which took many forms.

Think of Jesse like a showbiz parent who is always eager to give a quote to the press when their child is being wisely tight-lipped, or happy to scream, "don't you know who my son is!?" when at a Wendy's drive-thru. Ulysses, who had his own problems with military politicking and nosey reporters, had little patience for his father's antics. Jesse's letters to the press "defending" his son (he was really just taking the opportunity to make his own voice heard and to feel more important) were a constant headache to Ulysses. This got especially bad after the Battle of Shiloh, in the spring of 1862, at which point Ulysses pretty much forbid his dad from talking to the press any longer.

Always looking for a way to capitalize on his son's success and notoriety, though, Jesse was undeterred. Jesse took advantage of a new-ish Union policy that allowed cotton speculators to buy and sell southern cotton as long as they didn't do it in enemy (unoccupied) territory. This seems like a great idea on the surface, but in reality, what it did was create a headache for armies on the move, as cotton speculators were always waiting in the wings, hoping to swoop in on a newly "conquered" territory to buy/sell items that had previously been off-limits. Just imagine being a general in charge of thousands of troops and supply trains, planning your next move with the War Department and a president breathing down your neck, and on top of that, friggin' cotton speculators harassing you every free minute you've got so they can get permission to move into a nearby area. What's worse, people like Grant had to contend with officers in his own army making back-room deals with these same speculators to unofficially slip into certain areas in exchange for a cut of the action. Grant didn't need that headache, and when his dad showed up with a group of cotton speculators (who also happened to be Jewish) it seems he went nuclear.

Remember, when Gen. Order 11 was issued, Grant was having a tough time during the Vicksburg campaign. He hadn't yet devised his plan to ditch his supply lines and cross over the Mississippi River to attack Jackson, then Vicksburg itself: he was still trying (and failing) to devise other strategies to take the city/fort. He was less than a year removed from Shiloh, and was under a lot of pressure (some of it due to his dad's letters to the press).

So that's about where things were at when Gen. Order 11 came down. Ulysses, already frustrated with his father's meddling in his extremely serious affairs, blew a gasket. He chastised his father for assuming that Ulysses would use his military clout to help secure a cotton deal, and sent his dad and the speculators away on the first train leaving the area. In this fit of rage, he penned Gen. Order 11 in what appears to be a naked attempt to shift blame from his father (who he was actually angry at) to "this class of people." It was stupid, and wrong, and anti-Semitic, and everyone at the time knew it.

Lincoln had Grant's boss at the time, Gen. Halleck, order Grant to rescind the thing. Grant seems to have felt genuinely bad about the incident afterwards, though he rarely talked about it. As president, he appointed a number of Jewish officials (more than was normal at the time) and spoke out against Jewish persecution.

So, was it anti-Semitic even for the time? Absolutely. Did Grant harbor anti-Semitic sentiments? Well, from the text of Gen. Order 11, one has to think that he did to some degree, yes. Was Gen. Order 11 less about his anti-Semitism, and more about his long-running frustrations with his father? That's arguable, but I think there is a case to be made that this was indeed what was really in play. Which is not to excuse Grant's actions, here, but to provide a little more context to the event.

[Sources: 'Grant Moves South,' Bruce Catton; 'American Ulysses,' Ronald C. White]